chore: combine trace and function evidence prototypes

fix(cli): preserve partially captured source closure
fix(cli): retain function evidence sources in bundles
2026-11-07 17:34:14 -10:00 · 2026-11-04 14:29:02 +08:00 · 2026-11-04 14:26:17 +08:00 · 2026-11-04 14:24:09 +08:00 · 2026-11-04 14:17:15 +08:00 · 2026-11-04 14:06:59 +08:00
1886 changed files with 10493 additions and 139805 deletions
@@ -10,8 +10,8 @@ equivalent completed investigations. A useful outcome can also be a measured
 decision to leave an implementation alone.

 Follow the checkout's [performance priorities](../../../AGENTS.md#performance),
-[tool design](../../../docs/development/tool-design.md), and
-[testing guide](../../../docs/development/testing.md). This skill supplies an optimization
+[tool design](../../../docs/tool-design.md), and
+[testing guide](../../../docs/testing.md). This skill supplies an optimization
 workflow, not additional permission to execute targets, publish, or merge.
 Use the current contracts, provider prerequisites, and user authorization.

@@ -6,7 +6,7 @@ description: Prepare or rewrite REA release changelogs and GitHub release notes
 # REA changelog update

 Use this for release-note preparation and contributor attribution. Read
-[docs/development/releasing.md](../../../docs/development/releasing.md) from the repository root for
+[docs/releasing.md](../../../docs/releasing.md) from the repository root for
 publication authority and the existing checkpoint checks. This skill prepares
 notes; it does not authorize merging, tagging, or publishing.

@@ -9,7 +9,7 @@ Establish which checks still catch real regressions and which costs can be
 removed without losing that protection. The outcome may be a verified fix,
 an evidence-backed recommendation, or an explicit decision to stop.

-Follow the checkout's `AGENTS.md`, [testing guide](../../../docs/development/testing.md),
+Follow the checkout's `AGENTS.md`, [testing guide](../../../docs/testing.md),
 and [contribution rules](../../../CONTRIBUTING.md). Use their current commands
 and pinned toolchain, rather than commands remembered from an earlier audit.
 Preserve the requested scope: investigation alone does not authorize edits;
@@ -5,7 +5,7 @@ description: Audit, investigate, design, or change REA investigation tools, CLI/

 # REA tool design

-Use the [tool-design guide](../../../docs/development/tool-design.md) for tool boundaries,
+Use the [tool-design guide](../../../docs/tool-design.md) for tool boundaries,
 contract semantics, provider ownership, and discoverability. Inspect the current
 contract and nearest existing tool relevant to the analyst question; source,
 documentation, and live catalogs may describe different versions.
@@ -14,23 +14,21 @@ For provider-backed work, exercise the analyst's task through REA and compare
 relevant native provider and independent artifact observations where available.
 Check applicable partial results, recovery and session boundaries; report what
 was not exercised. For failure guidance, follow [design recovery around the
-failure](../../../docs/development/tool-design.md#design-recovery-around-the-failure).
-Use [workflow verification](../../../docs/development/testing.md#provider-backed-workflow-verification)
+failure](../../../docs/tool-design.md#design-recovery-around-the-failure).
+Use [workflow verification](../../../docs/testing.md#provider-backed-workflow-verification)
 to select evidence for the proposed contract instead of seeking provider API
 parity.

-For an audit, follow [audit existing tools](../../../docs/development/tool-design.md#audit-existing-tools):
+For an audit, follow [audit existing tools](../../../docs/tool-design.md#audit-existing-tools):
 scope representative tasks, exercise the live workflow, and distinguish
 reproduced bugs, supported limitations, design opportunities and unverified
-claims. Check relevant rendered MCP prompts, guided workflows and packaged skill
-advice against the live contracts and exercise their suggested handoffs. Report
-working alternatives and evidence limits as well as findings.
+claims. Report working alternatives and evidence limits as well as findings.

 For a design request, return the proposed boundary, input/result shape, Evidence
 semantics, nearest alternative, and verification approach. Implement when
 requested, preserving the user's scope and existing authorization.

-For implementation or verification, consult [testing](../../../docs/development/testing.md)
+For implementation or verification, consult [testing](../../../docs/testing.md)
 for the affected consumer and provider lanes, and
 [contributing](../../../CONTRIBUTING.md) for generated-file ownership. Read
 provider/workflow guides only as the task requires.
@@ -2,7 +2,7 @@
 name: reverse-engineer-anything
 description: Reverse engineer native, managed, Electron/JavaScript, packaged, firmware, and browser targets with REA, and build agent environments (AgentEnv bundles) of web applications from a live instance or a capture. Use shipped-artifact or requested runtime evidence to explain features, compare versions, decompile code, or guide a reconstruction. Skip REA for ordinary source-repository architecture analysis.
 metadata:
-  version: "60"
+  version: "59"
 ---

 # REA
@@ -108,7 +108,7 @@ explicit path or endpoint and do not need it.
 - Firmware image: `inspect_firmware_regions` when advertised. Use
  `extract_firmware` when extraction is requested, with a caller-selected new
  absolute output directory. These tools use caller-supplied Binwalk/Unblob on
-  Linux; see the [firmware guide](https://github.com/morluto/rea/blob/main/docs/guides/firmware/firmware-analysis.md).
+  Linux; see the [firmware guide](https://github.com/morluto/rea/blob/main/docs/firmware-analysis.md).
 - ESP32-family app or bootloader image (`0xE9` magic): `inspect_artifact`
  without a provider; see the ESP section of `references/native-and-artifacts.md`.
 - .NET NativeAOT PE/ELF: native Ghidra analysis. Native code can yield pseudocode;
@@ -121,15 +121,6 @@ explicit path or endpoint and do not need it.
  cleanup effects, and do not require a preliminary static session unless their
  own contract says so.
 - User-owned browser page already open: `list_browser_targets`.
- Passive traffic capture of a SPA: the default scope is the page's own origin,
-  and data APIs usually live on another origin. Discover API origins from
-  absolute URLs in loaded bundles or script text via JavaScript analysis tools
-  (another passive capture without those origins still scopes to the page
-  origin, and `completeness.excluded` counts lack URLs). Pass both the page
-  origin and those API origins in `allowed_origins` — the list replaces the
-  default scope — and read `completeness.excluded` before reporting that an
-  API is absent. For long captures with body shapes, use
-  `export_evidence_bundle` instead of expecting an inline result.
 - Browser action the agent must perform (click, type, navigate):
  `capture_browser_scenario` with declared actions. See
  [runtime observation](references/runtime-observation.md) for connect/launch
@@ -137,9 +128,6 @@ explicit path or endpoint and do not need it.
 - Agent environment (AgentEnv bundle) of a web application: read
  [environments](references/environments.md) before recording; it records with
  `capture_browser_scenario` and writes the bundle with `export_environment_bundle`.
- Task for a desktop application's exported environment, from a
-  `capture-desktop-application` folder: read
-  [desktop application tasks](references/environments.md#tasks-for-a-desktop-application-environment).
 - Fiddler Everywhere traffic or a native `.saz` capture: read the
  [Fiddler workflow](references/runtime-observation.md#fiddler-everywhere-traffic-debugging).
  Inspect saved SAZ with `inspect_web_network_capture` and `format: "saz"`;
@@ -150,7 +138,7 @@ explicit path or endpoint and do not need it.
  old-generation heap is `REA_CAPTURE_DECODER_OLD_GENERATION_MIB` (default 192 MiB,
  floor 8, maximum 16384), set where REA starts. Host memory and `NODE_OPTIONS` do not
  raise it. See
-  [historical captures](https://github.com/morluto/rea/blob/main/docs/guides/web/web-network-captures.md) for the exact upstream
+  [historical captures](https://github.com/morluto/rea/blob/main/docs/web-network-captures.md) for the exact upstream
  profile and credential exclusions. Qlog support starts with aioquic 1.5.0
  JSON 0.3; stream coverage and endpoint loss declarations do not recover bodies
  or establish network loss. Prefer detail summary, then kind qlog trace/stream
@@ -165,7 +153,7 @@ explicit path or endpoint and do not need it.
  display filters and decode-as rules. Requires Linux, util-linux prlimit and
  TShark 4.x on an absolute `PATH` entry or via the optional absolute
  `REA_TSHARK_COMMAND` override; see
-  [capture guide](https://github.com/morluto/rea/blob/main/docs/guides/data/packet-captures.md).
+  [capture guide](https://github.com/morluto/rea/blob/main/docs/packet-captures.md).
  Packet limits count input packets before filtering. Output defaults to 50 matching
  frames; use `match_offset` / `match_limit` for later pages, or explicit null
  limit for complete matching output. Preserve the source digest across pages.
@@ -173,7 +161,7 @@ explicit path or endpoint and do not need it.
  For address/DNS/SNI/protocol summaries use `inspect_pcap_capture` with MCP
  detail summary, then retained kind pcap pages. Requires Wireshark 4.x tshark
  and capinfos, with Linux prlimit or Windows Job Objects; see
-  [packet summaries](https://github.com/morluto/rea/blob/main/docs/guides/data/pcap-analysis.md).
+  [packet summaries](https://github.com/morluto/rea/blob/main/docs/pcap-analysis.md).
  Select an exact DNS question for address pages; page exhaustion does not prove
  network completeness. This reads recordings and does not acquire traffic.
 - Decoder discovery: `inspect_signal_decoders` searches installed decoder IDs
@@ -181,7 +169,7 @@ explicit path or endpoint and do not need it.
  relevant details before choosing settings; this does not scan hardware.
 - Recorded logic/signal traces: `decode_signal_recording` with explicit decoder,
  channel and protocol settings. On Linux with util-linux prlimit, supply sigrok-cli 0.7.2 through
-  `REA_SIGROK_COMMAND`; see [recording guide](https://github.com/morluto/rea/blob/main/docs/guides/signals/signal-recordings.md).
+  `REA_SIGROK_COMMAND`; see [recording guide](https://github.com/morluto/rea/blob/main/docs/signal-recordings.md).
  Output defaults to 50 literal lines; select annotation classes and page with
  `line_offset` / `line_limit`, or explicit null for all remaining output.
  Window counts are display lines, not annotations or samples. Preserve source digests across pages.
@@ -190,7 +178,7 @@ explicit path or endpoint and do not need it.
  through `REA_WABT_BIN_DIRECTORY`; retain exact byte/tool identity and decoded WAT.
  Select JavaScript glue and candidate paths explicitly and preserve URL/path
  ambiguity. No implicit fetch or target execution; WAT is not original source.
-  See the [WASM guide](https://github.com/morluto/rea/blob/main/docs/guides/wasm/wasm-artifacts.md).
+  See the [WASM guide](https://github.com/morluto/rea/blob/main/docs/wasm-artifacts.md).
 - Explicit local Android APK (or ZIP/AAB) signing: `inspect_apk_signature`.
  Prefer its summary or selected signer/digest/lineage page; retain complete
  Evidence and use `inspect_analysis_view` kind `apk-signature` for follow-ups.
@@ -209,13 +197,13 @@ explicit path or endpoint and do not need it.
  Evidence stays retained under its original identity. Use the returned
  `parent_evidence_id` for exact function or `bytecode_hex`/stdout/stderr pages.
  Candidate coverage does not establish interface completeness. See the
-  [EVM bytecode guide](https://github.com/morluto/rea/blob/main/docs/guides/evm/evm-bytecode.md).
+  [EVM bytecode guide](https://github.com/morluto/rea/blob/main/docs/evm-bytecode.md).
 - Embedded Go compiler, module or build-setting metadata: `inspect_go_binary`
  with the explicit local file. This built-in target-free inspection requires no
  Go installation or disassembler. Preserve raw module bytes and source ranges;
  absent metadata does not prove a binary is not Go, and unparsed text records
  remain explicit. See the
-  [Go binary guide](https://github.com/morluto/rea/blob/main/docs/guides/native/go-binaries.md).
+  [Go binary guide](https://github.com/morluto/rea/blob/main/docs/go-binaries.md).
 - Embedded CUDA/HIP code objects: `inspect_gpu_code_objects`; inventory targets
  first, then decode selected payloads and query retained GPU Evidence.
 - Bundled GGUF or safetensors model declarations: `inspect_model_artifact`
@@ -276,15 +264,6 @@ explicit path or endpoint and do not need it.
  linker declarations, not proof of enforcement. A missing directory is observed
  absence of that declaration. See the
  [PE load configuration guide](https://github.com/morluto/rea/blob/main/docs/pe-load-config.md).
- ELF, PE, and Mach-O hardening: `inspect_binary_hardening` with the explicit
-  local file. This built-in target-free inspection requires no pwntools or other
-  host tool. One image per Mach-O slice. Each property is `enabled`, `disabled`,
-  `partial`, `unknown`, or `not_applicable`, with the header field or import
-  behind it. A missing stack-protector or fortify import is `unknown`, not
-  proof the protection was omitted. Authenticode and Mach-O code signatures
-  report presence, not validity. Hardened runtime stays unknown and names
-  `inspect_signature`. The image is not executed. See the
-  [binary hardening guide](https://github.com/morluto/rea/blob/main/docs/binary-hardening.md).
 - ELF note tables: `inspect_elf_notes` with the explicit local ELF32/ELF64
  file. This built-in target-free inspection requires no disassembler. Preserve
  PT_NOTE and SHT_NOTE ranges, owners, types, descriptor SHA-256, and GNU
@@ -332,17 +311,17 @@ explicit path or endpoint and do not need it.
  20 rows; request `schema_scope: "database"` for the complete stored schema. Preserve both database and existing sibling WAL identity; row samples
  report truncation and have unspecified order. Use a quiescent snapshot rather
  than assuming a live database/WAL pair was copied atomically. See the
-  [SQLite guide](https://github.com/morluto/rea/blob/main/docs/guides/data/sqlite-databases.md).
+  [SQLite guide](https://github.com/morluto/rea/blob/main/docs/sqlite-databases.md).
 - Explicit Linux ELF file for offline layout, symbols, relocations or static
  mitigation evidence: `inspect_binary_layout`. This target-free operation uses
  caller-supplied pwntools without opening a disassembler database. Preserve its
  raw locations and inference/coverage limits; see the
-  [offline binary guide](https://github.com/morluto/rea/blob/main/docs/guides/native/binary-diagnostics.md).
+  [offline binary guide](https://github.com/morluto/rea/blob/main/docs/binary-diagnostics.md).
 - Supplied Linux x86-64 ELF core: `inspect_recorded_crash`. Read every recorded
  thread, raw note and source-bound register without opening a live target.
  Historical PIDs do not select live processes. Request `include_debugger_context`
  only when core-only mapping candidates help; see the
-  [recorded crash guide](https://github.com/morluto/rea/blob/main/docs/guides/native/recorded-crashes.md).
+  [recorded crash guide](https://github.com/morluto/rea/blob/main/docs/recorded-crashes.md).
 - PE resource type/name/language trees and static icon group references:
  `inspect_pe_resources` with an explicit path. This portable operation requires
  no active target or engine; opaque payloads retain file ranges and SHA-256.
@@ -358,9 +337,9 @@ The legacy attached profile binds the already-open GUI input by SHA-256 and
 leaves its database open. The modern headless profile creates and closes an
 owned private database without saving. Installation and registration reuse
 [mrexodia/ida-pro-mcp](https://github.com/mrexodia/ida-pro-mcp); see the
-[IDA provider guide](https://github.com/morluto/rea/blob/main/docs/providers/ida-provider.md).
+[IDA provider guide](https://github.com/morluto/rea/blob/main/docs/ida-provider.md).
 For migration to the separate native IDA MCP plugin, follow the guide's
-[legacy attached migration](https://github.com/morluto/rea/blob/main/docs/providers/ida-provider.md#migrate-a-legacy-attached-registration).
+[legacy attached migration](https://github.com/morluto/rea/blob/main/docs/ida-provider.md#migrate-a-legacy-attached-registration).
 Replace the upstream registration explicitly; modern mrexodia tools are not the
 native profile. Native attachment preserves the database but does not provide
 direct callers; check session availability and the guide's verification limits.
@@ -406,10 +385,6 @@ describe possible providers, while top-level session capabilities describe the
 current route and `analysis_provider_binding` names the selected provider. Do
 not treat those scopes as interchangeable.

-For editable Ghidra analysis that must survive a later agent process, select
-the [owned Program checkpoint workflow](references/native-and-artifacts.md#continue-editable-ghidra-analysis-across-processes)
-before making metadata edits. It is separate from Evidence/Unknown persistence.
-
 For a Ghidra startup timeout on a large native target, follow
 [deadline recovery](references/native-and-artifacts.md#ghidra-startup-deadline-recovery)
 before abandoning deep analysis or repeating the same cold import. The default
@@ -537,8 +512,6 @@ as complete while required questions remain open.
 - Agent environments (AgentEnv bundles) of a web application, recorded from
  a live instance or a HAR:
  [references/environments.md](references/environments.md)
- Tasks for a desktop application's exported environment:
-  [references/environments.md](references/environments.md#tasks-for-a-desktop-application-environment)

 ## Finish the task

@@ -22,7 +22,7 @@ Preserve slot/relocation provenance and source coverage: matched means observed
 candidate presence; partial scans do not establish uniqueness or absence.
 This reads DEX/ELF bytes without loading the APK into the decompiler or executing
 target code. Runtime registration and loading remain unknown. See the
-[JNI guide](https://github.com/morluto/rea/blob/main/docs/guides/android/android-analysis.md#link-native-declarations-to-jni-candidates).
+[JNI guide](https://github.com/morluto/rea/blob/main/docs/android-analysis.md#link-native-declarations-to-jni-candidates).

 For an R8/ProGuard release build with its `mapping.txt`, pass the absolute
 `mapping_path` to `inspect_android_class` or `inspect_android_method`. Prefer
@@ -11,7 +11,7 @@ main and an older release expose the same arguments. Tool-name prefixes belong
 to the client: find the canonical REA operation in its actual tool listing and
 server association before concluding that it is absent. A shared prefix alone
 does not establish which server an approval wildcard covers. See
-[client tool names and discovery](https://github.com/morluto/rea/blob/main/docs/getting-started/client-configuration.md#client-tool-names-and-discovery).
+[client tool names and discovery](https://github.com/morluto/rea/blob/main/docs/client-configuration.md#client-tool-names-and-discovery).

 ## Choose the remedy from the observed failure

@@ -8,9 +8,7 @@ confirmed. The workflow records the application once with
 again if a hint names a gap, then writes the bundle with
 `export_environment_bundle`. For a HAR the user already has, skip to
 [export](#export-and-hand-off) through `inspect_web_network_capture`, or use
-`rea environment-build <capture.har> <dir>`. For a task in a desktop
-application's exported environment, read
-[its section](#tasks-for-a-desktop-application-environment).
+`rea environment-build <capture.har> <dir>`.

 ## Before recording

@@ -287,90 +285,3 @@ See
 [agent environments](https://github.com/morluto/rea/blob/main/docs/agent-environments.md)
 for what the state, replay and the bundle establish, and
 [evidence workflows](evidence-workflows.md) for the manifest and state views.
-
-## Tasks for a desktop application environment
-
-Use this when the user has a folder from `rea capture-desktop-application` and
-wants a task for the environment `rea export-desktop-application` makes from
-it: a prompt for a computer-use agent and checks that grade what the agent
-left in the app's files. You write the prompt and the checks; REA validates
-the task against the capture and exports it. These commands are CLI only.
-
-### Describe the change
-
-Run `rea describe-desktop-application-task CAPTURE --format json`. Read:
-
- `owned_paths`: the only paths whose files the app serves, so the only files
-  a check can read.
- `files`: each file there whose state differs between the capture's first
-  and last version, with its `role`, the `baseline` and `final` versions and
-  the net `change`. Text changes list each added and removed line once, and
-  `line_counts` gives lines found at both ends whose count changed.
- `task`: a draft whose `checks` are suggestions from the net change of the
-  documents the user worked on, or of the app's own state when no document
-  changed.
-
-### Write the prompt
-
-Say what the user wants done, in their words and the app's terms: "Add buy
-milk to my to-do list and save it". Never say how the file stores it: no
-paths the user would not name, line formats, XML, keys or SQL, and never the
-checks. Replace the draft's placeholder; the export refuses it.
-
-### Pick the checks
-
-Checks must express only the observed change:
-
- Keep a suggestion only if it says what the user did. Drop those that follow
-  from how the app saves: a format rewrite, renumbered lines, counters. A
-  LibreCAD drawing gaining four holes was rewritten from DXF R12 to 2007, and
-  the draft suggests counts of `SECTION`, `ENDSEC` and `CIRCLE`; only
-  `CIRCLE` equals 9 is the user's change.
- Never check unchanged content, whole files, or values the app stamps:
-  times, ids it assigns, window sizes. REA refuses ISO 8601 and `asctime`
-  date-times (`Thu Nov  5 09:20:31 2026`); the
-  rest is your judgment.
- Prefer a few robust checks: whole lines over positions, rows by meaningful
-  columns over generated ids, `at_least` when the user may add more.
-
-Kinds: `file_present` and `file_absent`; `lines_present` and `lines_absent`
-(`lines`); `line_count` (`exact` or `contains`, and `equals`, `at_least` or
-`at_most`); `value_equals` and `value_absent` (a JSON `pointer` into the view,
-such as `/groups/GROUP/KEY` for a key file); `text_equals` and
-`text_contains` (an XML element's whole text at a `pointer`, optional
-`normalize_whitespace`); `row_present` and `row_absent` (`table`, `where` by
-column) and `row_count`. Each names its `file` as a path under the home. A
-document saved as a zip archive, such as FreeCAD's `.FCStd`, reads as its
-entries: point into an entry's view, and name array members by selector
-rather than position, as
-`/entries/[name=Document.xml]/view/root/children/[name=Object][@name=Hole]`,
-so the check survives an app version that writes them in another order. Give
-`value_equals` a `tolerance` to compare a number the app writes as text, such
-as `"5.0000000000000000"`, with a number. Check what the user wrote in a
-document with `text_equals` on its paragraph element, not `value_equals` on a
-text node: apps such as AbiWord and Writer split a paragraph into runs as they
-save, so its first text node holds only part of it; use `text_contains` for a
-value within a sentence, such as a time. The
-[desktop application tasks](https://github.com/morluto/rea/blob/main/docs/desktop-application-tasks.md)
-guide has the exact rules.
-
-### Export the task
-
-Write the task as JSON with a `name`, the `prompt` and the `checks`, then run
-`rea export-desktop-application CAPTURE DIRECTORY --task TASK.json`. REA keeps
-the task only when its checks fail on the seed and all pass on the captured
-end state. A refusal names the check: one that fails on the end state does not
-match what the user left; "every check already passes on the seed" means no
-check captures the change.
-
-When the export refuses an application that no apt repository installs, ask
-the user for the `.deb` file they installed it from and capture with
-`--package-file`, then ask where the computer may download that file and pass
-it as `--package-url`. Never fetch a vendor's download page yourself: such
-sites often refuse automated downloads, and the copy and its licence are the
-user's to choose.
-
-Tell the user the task's name, prompt and checks, and how to measure a solve
-rate: run `agent-env run DIRECTORY --task NAME --agent claude-code` with
-`--model MODEL` three times and count the runs reported `passed`. Do not run
-agents unless asked. The bundle's seed is the user's real data: keep it local.
@@ -47,7 +47,7 @@ member comparison CLI still takes two assembly paths; process comparison takes
 two capture Evidence JSON paths. Check command help for the installed version.
 An input bundle grants no implicit file lookup: `evidence-file` and historical
 graph file selectors are accepted only by contracts advertising them. See the
-[CLI reuse guide](https://github.com/morluto/rea/blob/main/docs/getting-started/cli.md#import-export-and-compare-evidence).
+[CLI reuse guide](https://github.com/morluto/rea/blob/main/docs/cli.md#import-export-and-compare-evidence).

 Completed `inspect_artifact` inventory also supports a summary and
 `view: {kind: "inventory", collection: "occurrences", logical_paths: ["package.json", "main.js"]}`.
@@ -6,7 +6,7 @@ For captured or bundled JavaScript that needs readable source recovery, use
 `additional_paths` when advertised, then analyze the returned `analysis_input`
 directory together. Each input retains its own snapshot, digest and byte-range
 provenance; inputs and recovered code are never executed. Recovery requires a
-caller-supplied Wakaru on Linux x64; see [the recovery guide](https://github.com/morluto/rea/blob/main/docs/guides/javascript/javascript-recovery.md).
+caller-supplied Wakaru on Linux x64; see [the recovery guide](https://github.com/morluto/rea/blob/main/docs/javascript-recovery.md).

 Use `analyze_javascript_application` directly on the operator-supplied ASAR or
 extracted tree. When the question concerns known source paths and the connected
@@ -155,18 +155,6 @@ mitigations carry `evidence_kind: "inferred"`; enforcement remains unobserved.
 See
 [PE TLS callbacks and load configuration](https://github.com/morluto/rea/blob/main/docs/pe-load-config.md).

-## Binary hardening
-
-Use `inspect_binary_hardening` for an explicit local ELF, PE, or Mach-O file
-when the question concerns PIE or ASLR, NX, RELRO, stack-protector or FORTIFY
-signs, control-flow flags, or stripped state. No `open_binary`, pwntools, or
-target execution is required. The CLI equivalent is
-`inspect-binary-hardening PATH`. Universal Mach-O files return one image per
-slice. A missing import is `unknown`, not proof the protection was omitted.
-Authenticode and Mach-O code-signature rows report presence, not validity.
-`hardened_runtime` stays unknown and names `inspect_signature`. See
-[binary hardening](https://github.com/morluto/rea/blob/main/docs/binary-hardening.md).
-
 ## ELF note tables

 Use `inspect_elf_notes` for an explicit local ELF32/ELF64 image when the
@@ -246,7 +234,7 @@ Choose `row_limit` when a finite sample is useful and keep truncation and
 unspecified row order explicit. Virtual tables, shadow tables and views are
 schema facts, not row-read targets. REA inspects private copies and leaves
 the source files untouched; obtain a coherent quiescent database/WAL snapshot
-before inspection. See [SQLite snapshots](https://github.com/morluto/rea/blob/main/docs/guides/data/sqlite-databases.md).
+before inspection. See [SQLite snapshots](https://github.com/morluto/rea/blob/main/docs/sqlite-databases.md).

 ## Recorded Linux crashes

@@ -261,7 +249,7 @@ The optional `include_debugger_context` facet adds mapping candidates through
 caller-supplied GDB/pwndbg in an owned core-only session. Display names do not
 establish current file identity; zero reported flags leave permissions unknown.
 Requested unavailable context fails with setup guidance. See
-[recorded crashes](https://github.com/morluto/rea/blob/main/docs/guides/native/recorded-crashes.md)
+[recorded crashes](https://github.com/morluto/rea/blob/main/docs/recorded-crashes.md)
 for exact upstream profiles, bounds and verification coverage.

 ## Offline ELF layout
@@ -320,18 +308,6 @@ cross-references. Addresses and recovered pseudocode are analysis observations,
 not original source. Provider unavailability and unsupported metadata remain
 unknown rather than false.

-For large pseudocode, request `procedure_pseudo_code` with `detail: "summary"`
-on the first MCP call. It retains the complete observation and returns the
-original selection, text availability and length without the body. Use
-`normalized_result.parent_evidence_id` with `inspect_analysis_view` and
-`view: {kind: "native", facet: "pseudocode", offset: 0, limit: 20000}`;
-follow `coverage.next_offset` for later pages. Choose a smaller limit if one
-page exceeds the client or transport budget. Offsets and limits count UTF-16
-code units, not lines or tokens. Pages reuse the same observation without
-repeating decompilation. Null and empty text remain distinct. Omitted or
-`complete` detail preserves full inline delivery. Summary delivery requires a
-retaining session and does not reduce the work or memory of decompilation.
-
 For a completed `analyze_function` dossier, use `inspect_analysis_view` with
 `view: {kind: "native", facet: "value_flow_operations", offset: 0, limit: 32}`
 and the exact retained Evidence ID to read selected facts without reanalysis.
@@ -382,28 +358,6 @@ operation's full ordered list. Candidate capabilities, returned with complete
 detail, describe possible providers. Top-level session capabilities describe the current route, and
 `analysis_provider_binding` identifies the selected provider.

-## Continue editable Ghidra analysis across processes
-
-For a task spanning agent sessions, check `binary_session` after selecting
-Ghidra: the current provider's `capabilities[].shared_limitations` states whether
-Program checkpoints are enabled or the session is ephemeral. Successful native
-queries distinguish initial analysis from an actually restored packed Program;
-do not infer that restoration happened merely because checkpoint mode is enabled.
-
-In ephemeral mode, choose a private absolute directory and set
-`REA_GHIDRA_CHECKPOINT_DIR` in the environment starting REA. Restart the MCP server
-after changing that launch configuration; no current tool call or runtime
-analysis-setting update enables it. Stock ELF/PE/Mach-O imports on Linux/macOS
-are supported; see the [checkpoint setup and limitations](https://github.com/morluto/rea/blob/main/docs/getting-started/installation.md#automatically-checkpoint-an-owned-ghidra-program).
-
-With the setting enabled, normal opens restore compatible saved Programs
-automatically. Initial completed analysis is saved, and `close_binary` saves
-later metadata edits; no separate save/restore tool is needed. Repair a reported
-save failure and retry close. Cancellation or process failure can lose edits
-after the last successful save; unfinished initial analysis cannot resume.
-Keep the same checkpoint configuration for later processes. Evidence/Unknown
-history and immutable REA query snapshots have separate persistence workflows.
-
 ## Reuse caller-selected Ghidra analysis

 When the caller supplies an expanded project, configure `REA_GHIDRA_PROJECT_PATH`
@@ -415,7 +369,7 @@ import overrides and repair scripts are unavailable in this mode. Treat original
 analysis completeness/settings as unknown and prior edits as caller-project state.
 The program's recorded import digest must match the target; changed project content
 requires reopening for a fresh profile. See the
-[setup and preparation guide](https://github.com/morluto/rea/blob/main/docs/getting-started/installation.md#reuse-an-existing-ghidra-project).
+[setup and preparation guide](https://github.com/morluto/rea/blob/main/docs/installation.md#reuse-an-existing-ghidra-project).

 ## Ghidra startup deadline recovery

@@ -427,7 +381,7 @@ When the error names `ghidra.startup_timeout_ms`, call
 `update_analysis_settings` with `action: "set"` and a larger value within the
 reported bounds. Resolve retained cleanup before the next startup attempt.
 No REA restart is needed; an already accepted startup keeps its original
-budget. Follow the error's session-specific restart guidance, and preserve useful Evidence before closing
+budget. A new attempt repeats import. Preserve useful Evidence before closing
 and reopening the target when remediation requires that lifecycle step.

 For a per-function timeout, update `ghidra.decompile_timeout_seconds` and retry
@@ -449,7 +403,7 @@ and memory controls in place. Disable specific expensive analyzers only when
 their missing coverage is acceptable and retain the resulting limitations.
 Exported C and embedded resources remain useful independent evidence, but a
 timeout does not establish complete analysis or absence of code. See the
-[deadline and client guide](https://github.com/morluto/rea/blob/main/docs/reference/mcp-contracts.md#ghidra-first-query-deadlines-and-recovery).
+[deadline and client guide](https://github.com/morluto/rea/blob/main/docs/mcp-contracts.md#ghidra-first-query-deadlines-and-recovery).

 ## Bridge request ceiling

@@ -600,7 +554,7 @@ broader metadata recovery on Linux; it requires an explicitly configured
 NativeAOT JAR. These are separate routes. The built-in parser also runs on
 Windows Ghidra P0; read frozen literals from its report, because
 `search_strings` does not include them. See the
-[NativeAOT guide](https://github.com/morluto/rea/blob/main/docs/providers/ghidra-nativeaot.md)
+[NativeAOT guide](https://github.com/morluto/rea/blob/main/docs/ghidra-nativeaot.md)
 for setup, supported layouts, and host restrictions. Preserve binary identity
 and distinguish derived metadata from Ghidra database observations. Recovered
 types and native pseudocode are not original C# source. Windows Ghidra P0 has
@@ -629,7 +583,7 @@ every executable in the bundle. It also lists missing or weak loads and earlier
 provides them.

 Use `extract_artifact` when materialized files from a supported format are needed.
-It extracts the active target and accepts optional `integrity_policy`; see the [MCP contracts](https://github.com/morluto/rea/blob/main/docs/reference/mcp-contracts.md).
+It extracts the active target and accepts optional `integrity_policy`; see the [MCP contracts](https://github.com/morluto/rea/blob/main/docs/mcp-contracts.md).
 It materializes all regular files into a fresh temporary directory chosen by
 REA. Symlinks and encrypted entries are inventory facts, not extractable files.
 The result reports the materialized directory; callers do not choose the
@@ -657,7 +611,7 @@ temporary, not a retained export of the image's contents.
 For headerless DOS COM, explicitly open with `format: "dos-com"` (CLI
 `--target-format dos-com`). Inspect the load image before trusting function
 analysis: the entry is `0x10100`, file offset zero, with imposed real-mode segment
-context. PSP/stack/device state remains unmodeled. See [DOS guide](https://github.com/morluto/rea/blob/main/docs/providers/ghidra-dos.md).
+context. PSP/stack/device state remains unmodeled. See [DOS guide](https://github.com/morluto/rea/blob/main/docs/ghidra-dos.md).

 Use `inspect_byte_entropy` to triage high- and low-entropy ranges before extraction.

@@ -671,7 +625,7 @@ otherwise. Big-endian ARM, Thumb-only, and Cortex-M variants are unsupported.
 `0x0000..0xffff`. 65C02, 65816, cartridge containers, bank switching, and mapper
 semantics are unsupported. `m68k` requires an even entry and decodes the 68040
 superset of the 68000 family; Amiga/Atari containers and vector-table entry
-discovery are unsupported. Windows Ghidra P0 admits raw images only for `6502`. See [raw binary guide](https://github.com/morluto/rea/blob/main/docs/providers/raw-binary.md).
+discovery are unsupported. Windows Ghidra P0 admits raw images only for `6502`. See [raw binary guide](https://github.com/morluto/rea/blob/main/docs/raw-binary.md).

 Intel HEX, S-record, UF2 and DfuSe files are containers, not raw images:
 `inspect_artifact` lists address regions (UF2 per familyID, DfuSe per element
@@ -683,12 +637,7 @@ numbering gaps leave coverage unknown; a DfuSe suffix CRC mismatch follows
 ### Function annotations in Ghidra

 Fresh-import sessions admit annotations; existing-project reuse is read-only.
-Use `annotate_native_function` for one function name and/or entry comments, with at least one explicit change. Review its annotation readback and refreshed dossier inline. Changes are atomic; empty comments clear them, omitted fields preserve them. Later MCP calls observe edits. Normal close saves them when owned Program checkpoint mode is enabled; ephemeral mode discards them. CLI `annotate-native-function` follows the same setting when closing after its updated result. Select the [checkpoint workflow](#continue-editable-ghidra-analysis-across-processes) before edits that must survive a later process. Original executable bytes are unchanged; edits invalidate immutable snapshots. Windows P0 does not admit database mutations. For naming only, `set_address_name` / `set_addresses_names` also work with Ghidra: they name function entries or data addresses (primary labels) and return compact per-address success booleans instead of a dossier. Ghidra rejects batch addresses that request the same name or a name another selected address holds; `raw_result.failures` gives each failure's reason.
-
-A provider switch or different target can retire the active Ghidra database and discard
-its edits, even if the new provider fails on a later call. Same-target,
-same-profile reopen keeps the active database. Retained annotation Evidence
-records what happened; it does not restore the edits.
+Use `annotate_native_function` for one function name and/or entry comments, with at least one explicit change. Review its annotation readback and refreshed dossier inline. Changes are atomic and session-scoped; empty comments clear them, omitted fields preserve them. Later MCP calls observe edits until close. CLI `annotate-native-function` returns the updated analysis before discarding the session. Original executable bytes are unchanged; edits invalidate immutable snapshots. Windows P0 does not admit database mutations. For naming only, `set_address_name` / `set_addresses_names` also work with Ghidra: they name function entries or data addresses (primary labels) and return compact per-address success booleans instead of a dossier. Ghidra rejects batch addresses that request the same name or a name another selected address holds; `raw_result.failures` gives each failure's reason.

 For `compare_functions`, obtain `analyze_function` Evidence before and after the
 edit while the MCP session is open; annotation Evidence is not a comparison
@@ -710,7 +659,7 @@ code pages, payload hashes and static icon-group references. Same-language icon
 resolution is explicit; missing references and size mismatch remain visible.
 Other payloads are opaque, and this operation does not decode images or simulate
 Windows resource loading. Consult the budgets and supported tree profile in
-[offline binary diagnostics](https://github.com/morluto/rea/blob/main/docs/guides/native/binary-diagnostics.md).
+[offline binary diagnostics](https://github.com/morluto/rea/blob/main/docs/binary-diagnostics.md).

 ## Offline PE and ELF export tables

@@ -720,7 +669,7 @@ directory or ELF dynamic symbol table on any host without opening a native
 target. Ordinal-only, forwarded and hidden-version exports stay distinct;
 partial or unsupported coverage means the inventory is incomplete, not that
 exports are absent. Use `inspect_macho` for Mach-O. See
-[offline binary diagnostics](https://github.com/morluto/rea/blob/main/docs/guides/native/binary-diagnostics.md).
+[offline binary diagnostics](https://github.com/morluto/rea/blob/main/docs/binary-diagnostics.md).

 For exact core-module import/export differences, use `compare_wasm_interfaces`
 with two complete inspection Evidence records (or current-session retained
@@ -759,13 +708,6 @@ cache one decoded block and support retained filtered/paged views. No
 decryption or SerializedFile object decoding is provided. See
 [UnityFS](https://github.com/morluto/rea/blob/main/docs/unityfs.md).

-WeChat mini-program packages (`.wxapkg` files with `0xBE`/`0xED` marks) list
-members with declared names and absolute carrier offsets; member bytes are
-stored verbatim. `V1MMWX` PC-client packages report `encrypted` directory
-status with unknown coverage and are refused on extraction; no decryption is
-attempted. See
-[wxapkg](https://github.com/morluto/rea/blob/main/docs/wxapkg.md).
-
 U-Boot legacy uImages use the same inspection/extraction workflows. Prefer a
 retained summary and selected inventory views for header facts or component
 IDs. Header addresses/CPU/OS are declarations; payloads remain as stored.
@@ -41,10 +41,10 @@ behavior unknown. Record truncation, unmatched breakpoints, changed target
 identity and cleanup uncertainty as limitations, rather than treating no retained
 event as proof that the behavior never occurs.

-Detailed contracts and prerequisites: [Frida](https://github.com/morluto/rea/blob/main/docs/guides/runtime/frida-instrumentation.md),
+Detailed contracts and prerequisites: [Frida](https://github.com/morluto/rea/blob/main/docs/frida-instrumentation.md),
 [GDB/Rizin/Cutter](https://github.com/morluto/rea/blob/main/docs/reverse-engineering-tools.md),
-[process capture](https://github.com/morluto/rea/blob/main/docs/guides/runtime/process-capture.md),
-and [native calls/UI](https://github.com/morluto/rea/blob/main/docs/guides/native/native-investigation.md#native-desktop-observation).
+[process capture](https://github.com/morluto/rea/blob/main/docs/process-capture.md),
+and [native calls/UI](https://github.com/morluto/rea/blob/main/docs/native-investigation.md#native-desktop-observation).

 ## Browser and Electron

@@ -130,5 +130,5 @@ Inspect native `.saz` snapshots with `inspect_web_network_capture` and
 traffic analysis, connect Everywhere's separate MCP server and use its
 advertised session tools with an explicit `sessionsSource` (`LiveTraffic` or
 `AgentCalls`). Preserve existing sessions and filters when inspecting a
-recorded run. See the [capture and MCP guide](https://github.com/morluto/rea/blob/main/docs/guides/web/web-network-captures.md)
+recorded run. See the [capture and MCP guide](https://github.com/morluto/rea/blob/main/docs/web-network-captures.md)
 for the workflow and Telerik's public setup and traffic-debugging skills.
@@ -27,7 +27,7 @@ body:
    attributes:
      label: Documentation location
      description: Link the page, section, command, API, skill, or inline comment.
-      placeholder: README.md#quick-start or docs/reference/mcp-contracts.md
+      placeholder: README.md#quick-start or docs/mcp-contracts.md
    validations:
      required: true

@@ -71,8 +71,8 @@ source, link, or rendered-document checks. -->
 - User-visible CLI/MCP output (if applicable):
 - Remaining proof gaps:

-For boundary fixes, identify the applicable [boundary regressions](https://github.com/morluto/rea/blob/main/docs/development/testing.md#boundary-regressions)
-and [lifecycle regressions](https://github.com/morluto/rea/blob/main/docs/development/testing.md#lifecycle-regressions)
+For boundary fixes, identify the applicable [boundary regressions](https://github.com/morluto/rea/blob/main/docs/testing.md#boundary-regressions)
+and [lifecycle regressions](https://github.com/morluto/rea/blob/main/docs/testing.md#lifecycle-regressions)
 covered by the evidence above, and explain relevant gaps.

 For evidence-bearing changes:
@@ -99,7 +99,7 @@ limits, security/privacy/containment implications, and meaningful proof gaps. --
  its new behavior and migration, and why compatibility/deprecation cannot
  preserve it. Every release increments minor, including breaking changes;
  keep breaking markers and migration notes so callers can assess compatibility.
-  See docs/development/releasing.md. -->
+  See docs/releasing.md. -->
 - Real Hopper/Ghidra, browser, or OS coverage:
 - Package or release metadata impact:
 - Security, privacy, process, or containment review:
@@ -1016,8 +1016,8 @@ jobs:
        uses: ./.github/actions/npm-cache
      - run: npm ci
      - run: npm run docs:check
-      - name: Verify published routes, source links and local anchors
-        run: npm run verify:docs:routes
+      - name: Render documentation and validate page links
+        run: npm run docs:build
      - name: Generation leaves authored files unchanged
        run: git diff --exit-code
      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2
@@ -27,4 +27,4 @@ jobs:
        id: npm-cache
        uses: ./.github/actions/npm-cache
      - run: npm ci
-      - run: npm run verify:docs:routes
+      - run: npm run docs:build
@@ -54,11 +54,10 @@ jobs:
      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
        with:
          python-version: "3.12"
-      # The pinned framework builds its gateway and service-db images only when pulling them from
-      # ghcr.io fails, from public ECR base images; public ECR caps anonymous pulls by data per source
-      # IP and hosted runners share IPs, so such a build can fail here for hours. mirror.gcr.io serves
-      # the same Docker official images under the same digests, so each base image those Dockerfiles
-      # name is pulled there and named as its Dockerfile names it, as the framework's own CI does.
+      # Public ECR caps anonymous pulls by data per source IP and hosted runners share IPs, so the
+      # framework's image builds can fail here for hours. mirror.gcr.io serves the same Docker
+      # official images under the same digests, so each base image the pinned framework builds from
+      # is pulled there and named as its Dockerfile names it, as the framework's own CI does.
      # Digest-pinned names are set in containerd, whose images Docker reads only on the containerd
      # image store; switching stores restarts dockerd, so it happens before anything uses Docker.
      - name: Use the containerd image store
@@ -73,16 +72,16 @@ jobs:
        run: |
          runner_root="${RUNNER_TEMP}/rea-agentenv-runner"
          python -m venv "${runner_root}"
-          "${runner_root}/bin/python" -m pip install --require-virtualenv --no-cache-dir 'agentenv-framework==0.9.1431'
+          "${runner_root}/bin/python" -m pip install --require-virtualenv --no-cache-dir 'agentenv-framework==0.9.1334'
          "${runner_root}/bin/agent-env" --version
          docker version --format '{{.Server.Version}}'
          echo "REA_AGENT_ENV_COMMAND=${runner_root}/bin/agent-env" >> "${GITHUB_ENV}"
          echo "REA_DOCKER_COMMAND=$(command -v docker)" >> "${GITHUB_ENV}"
-      - name: Pull the gateway and service-db public ECR base images from mirror.gcr.io
+      - name: Pull the pinned framework's public ECR base images from mirror.gcr.io
        shell: bash
        run: |
          package="$("${REA_AGENT_ENV_COMMAND%/agent-env}/python" -c 'import agent_env, pathlib; print(pathlib.Path(agent_env.__file__).parent)')"
-          grep -rhoE '^FROM +public\.ecr\.aws/docker/library/[^ ]+' --include='Dockerfile*' "${package}/env/gateway" "${package}/env/envs/service_db" | awk '{print $2}' | sort -u |
+          grep -rhoE '^FROM +public\.ecr\.aws/docker/library/[^ ]+' --include='Dockerfile*' "${package}" | awk '{print $2}' | sort -u |
            while read -r image; do
              name=${image#public.ecr.aws/docker/library/}
              source=mirror.gcr.io/library/$name
@@ -14,13 +14,13 @@ Preserve caller-selected inputs and local evidence, including output, URLs, path

 ## Architecture and Cleanup

-Dependencies flow inward: domain semantics and contracts, provider adapters, shared application workflows, then CLI/MCP adapters. Keep engine protocols and provider-specific code out of domain/application layers. See [docs/architecture/architecture.mermaid](docs/architecture/architecture.mermaid) when changing composition.
+Dependencies flow inward: domain semantics and contracts, provider adapters, shared application workflows, then CLI/MCP adapters. Keep engine protocols and provider-specific code out of domain/application layers. See [docs/architecture.mermaid](docs/architecture.mermaid) when changing composition.

 Give each interpretation and resource a clear owner. Consumers must use that owner's parsed facts rather than reinterpret raw source. Preserve identity, omission, uncertainty, and source evidence across boundaries. Retain ownership of resources whose cleanup failed. Reuse `src/process/` supervision and identity primitives; a PID and executable path alone do not establish ownership after exit or reuse.

 Keep proof of ownership separate from validity, editability, and readiness. Malformed owned data may still be safely removable. Unresolved identity or applicability must remain unknown rather than be treated as absent, foreign, or aligned.

-For lifecycle changes, follow [ownership and completion invariants](docs/development/tool-design.md#own-the-lifecycle) and select the applicable [lifecycle regressions](docs/development/testing.md#lifecycle-regressions). Include late handshakes, cancellation during final cleanup, mixed child outcomes, and cleanup retry where those stages exist; active-execution cancellation alone does not cover finalization.
+For lifecycle changes, follow [ownership and completion invariants](docs/tool-design.md#own-the-lifecycle) and select the applicable [lifecycle regressions](docs/testing.md#lifecycle-regressions). Include late handshakes, cancellation during final cleanup, mixed child outcomes, and cleanup retry where those stages exist; active-execution cancellation alone does not cover finalization.

 Before adding complexity for a speculative or vanishingly unlikely race or security edge case, explain the concrete failure mode, likelihood, and complexity cost to the user and get their buy-in. Do not silently expand scope for theoretical robustness.

@@ -68,12 +68,6 @@ do not establish fewer tokens or faster analysis.

 ## Development

-Documentation ownership and authoring conventions live in
-[docs/development/documentation.md](docs/development/documentation.md). A feature
-uses `docs/specs/<domain>/<feature-slug>/spec.md`, one `plan.md` and `tasks.md`;
-individual architectural decisions use `docs/adr/<domain>/<decision-slug>.md`.
-Consult the [documentation directory](docs/README.md) before adding a guide.
-
 Use [.nvmrc](.nvmrc) and `package.json#packageManager` for the pinned toolchain. Cursor Cloud may place older Node.js first on `PATH`; environment setup installs the pinned toolchain under `/usr/local/bin`. Prefix `PATH="/usr/local/bin:$PATH"` before `node` and `npm`.

 - `npm ci`: install locked dependencies.
@@ -86,15 +80,15 @@ Use [.nvmrc](.nvmrc) and `package.json#packageManager` for the pinned toolchain.
 Use relevant checks for the change. The complete local gate, `npm run check:pr`, is optional for broad changes or CI diagnosis. See [CONTRIBUTING.md](CONTRIBUTING.md) for development, generated-file ownership, and release conventions.

 When changing installers or setup recovery, follow
-[Checking installers and publisher downloads](docs/development/testing.md#checking-installers-and-publisher-downloads).
+[Checking installers and publisher downloads](docs/testing.md#checking-installers-and-publisher-downloads).

-Coordinate expensive checks across agents. If a test unexpectedly consumes heavy CPU, stop its owned process family and profile a bounded representative case before retrying. Inspect production work, fixture generation, subprocesses, and repeated setup; preserve regression coverage when optimizing. Follow the [test resource guidance](docs/development/testing.md#developer-commands).
+Coordinate expensive checks across agents. If a test unexpectedly consumes heavy CPU, stop its owned process family and profile a bounded representative case before retrying. Inspect production work, fixture generation, subprocesses, and repeated setup; preserve regression coverage when optimizing. Follow the [test resource guidance](docs/testing.md#developer-commands).

 `docs/public/product-catalog.json`, `docs/verification/managed-conformance-*.json`, and `skills/` are ignored outputs. Edit source contracts and `.agents/skills/reverse-engineer-anything/`, then regenerate as needed. `.cache/mcp-tool-catalog.json` is test metadata; runtime builds and source checking do not consume it. Never commit binaries, provider project documents, credentials, `dist/`, `node_modules/`, or local planning artifacts.

 ## Tool and Test Changes

-For tool design, follow [docs/development/tool-design.md](docs/development/tool-design.md): start from the analyst question, reuse existing contracts, preserve caller choices, and return useful evidence inline. Limits must follow real format, protocol, authority, or resource constraints. Account for representation expansion before allocation; derive completeness from examined coverage.
+For tool design, follow [docs/tool-design.md](docs/tool-design.md): start from the analyst question, reuse existing contracts, preserve caller choices, and return useful evidence inline. Limits must follow real format, protocol, authority, or resource constraints. Account for representation expansion before allocation; derive completeness from examined coverage.

 For user- or agent-facing tool problems, prioritize fixing the owning behavior,
 contract, and actionable result or recovery at the point of use. Document the
@@ -102,7 +96,7 @@ result in product docs when explanation is needed. Add skill guidance only for
 workflow judgment or context that the tool cannot reasonably convey; do not use
 a skill as the primary repair for a discoverability or contract defect.

-For test changes or provider claims, use [docs/development/testing.md](docs/development/testing.md). Select applicable [boundary regressions](docs/development/testing.md#boundary-regressions) for parser, inventory, snapshot, and projection fixes. Prefer real public CLI/MCP workflows, then production-boundary integration, then producer goldens. Keep module tests for distinct semantics stronger workflows cannot reliably reproduce. Preserve malformed-input, cancellation, cleanup, permission, capacity, and target-identity coverage when pruning. Report unverified coverage explicitly; simulated providers do not establish real-provider behavior.
+For test changes or provider claims, use [docs/testing.md](docs/testing.md). Select applicable [boundary regressions](docs/testing.md#boundary-regressions) for parser, inventory, snapshot, and projection fixes. Prefer real public CLI/MCP workflows, then production-boundary integration, then producer goldens. Keep module tests for distinct semantics stronger workflows cannot reliably reproduce. Preserve malformed-input, cancellation, cleanup, permission, capacity, and target-identity coverage when pruning. Report unverified coverage explicitly; simulated providers do not establish real-provider behavior.

 Use Conventional Commit subjects and PR titles. Mark breaking changes with `!` or a `BREAKING CHANGE:` footer. Describe behavior changes, relevant validation, and real-provider verification scope.

@@ -132,8 +132,8 @@ Full contribution record: [4 commits and 1 merged PR](https://github.com/morluto
 - **Kuna analysis:** Use a caller-installed Kuna for procedure listings, pseudocode, assembly, call relationships, exact-address xrefs and cached string searches. Project exports retain source spans and digests; repeated requests reuse completed work. Recorded real-provider coverage uses Kuna 1.833 on Linux; Windows, PE and universal Mach-O are unsupported. See [the provider guide](docs/kuna-provider.md). ([#3832](https://github.com/morluto/rea/pull/3832), [#3854](https://github.com/morluto/rea/pull/3854), [#4071](https://github.com/morluto/rea/pull/4071), [#4095](https://github.com/morluto/rea/pull/4095)). Thanks @gensokyo-dev, @kaoru0822-kitauji, @N0zoM1z0.
 - **Retained JavaScript facts:** Query exact application paths, selected properties and filtered module references through `inspect_analysis_view`, with paging and complete row Evidence. These views reuse completed analysis and preserve source selection and unknown coverage. ([#4265](https://github.com/morluto/rea/pull/4265), [morluto/rea#4190](https://github.com/morluto/rea/issues/4190), [#4097](https://github.com/morluto/rea/pull/4097), [morluto/rea#4092](https://github.com/morluto/rea/issues/4092)). Thanks @kaoru0822-kitauji, @N0zoM1z0.
 - **APK locale tables:** Request several resource locales in one decode with repeatable CLI `--locales` or MCP `locales`. Each table reports its status and coverage; existing single-locale fields remain available. ([#4804](https://github.com/morluto/rea/pull/4804), [morluto/rea#4777](https://github.com/morluto/rea/issues/4777)). Thanks @abhay-2108, @N0zoM1z0.
- **Windows ARM binaries:** Ghidra admits ARMNT/Thumb-2 and ARM64 PE applications and DLLs on the Windows x64 host lane. Recorded Ghidra 12.1.4 verification uses `WindowsResourceReference` disabled and raised startup budgets; default-analyzer completion, ARM64EC/ARM64X and Windows-on-Arm hosts remain unverified or unsupported. See [the exact scope](docs/providers/windows-ghidra-p0.md#native-authority-and-target-identity). ([#3965](https://github.com/morluto/rea/pull/3965), [morluto/rea#2186](https://github.com/morluto/rea/issues/2186)). Thanks @N0zoM1z0, @WestLabsAI.
- **Raw m68k images:** Analyze explicitly selected big-endian m68k raw binaries using Ghidra’s fixed 68000 profile and a caller-supplied aligned entry. Real CLI/MCP verification used Ghidra 12.1.4 on macOS arm64; Linux is unverified and Windows P0 does not admit m68k. See [mapping requirements](docs/providers/raw-binary.md). ([#4018](https://github.com/morluto/rea/pull/4018)). Thanks @icedac.
+- **Windows ARM binaries:** Ghidra admits ARMNT/Thumb-2 and ARM64 PE applications and DLLs on the Windows x64 host lane. Recorded Ghidra 12.1.4 verification uses `WindowsResourceReference` disabled and raised startup budgets; default-analyzer completion, ARM64EC/ARM64X and Windows-on-Arm hosts remain unverified or unsupported. See [the exact scope](docs/windows-ghidra-p0.md#native-authority-and-target-identity). ([#3965](https://github.com/morluto/rea/pull/3965), [morluto/rea#2186](https://github.com/morluto/rea/issues/2186)). Thanks @N0zoM1z0, @WestLabsAI.
+- **Raw m68k images:** Analyze explicitly selected big-endian m68k raw binaries using Ghidra’s fixed 68000 profile and a caller-supplied aligned entry. Real CLI/MCP verification used Ghidra 12.1.4 on macOS arm64; Linux is unverified and Windows P0 does not admit m68k. See [mapping requirements](docs/raw-binary.md). ([#4018](https://github.com/morluto/rea/pull/4018)). Thanks @icedac.
 - **JADX deadlines:** Set `REA_JADX_OPERATION_TIMEOUT_MS` to extend APK loading and upstream operation deadlines together. Doctor reports the effective value and setup forwards an explicit selection. ([#4466](https://github.com/morluto/rea/pull/4466), [morluto/rea#3918](https://github.com/morluto/rea/issues/3918)). Thanks @jaychou813, @SandstromPL.
 - **Electron window options:** Resolve stable local constant `BrowserWindow` options while retaining source provenance. Relevant writes and escapes keep the result unknown. ([#4400](https://github.com/morluto/rea/pull/4400), [morluto/rea#4366](https://github.com/morluto/rea/issues/4366)). Thanks @kaoru0822-kitauji, @N0zoM1z0.
 - **Language editions:** Add the Greek website edition and Malayalam documentation, with Korean typography and translation corrections across the site. ([#3520](https://github.com/morluto/rea/pull/3520), [#4792](https://github.com/morluto/rea/pull/4792), [#3821](https://github.com/morluto/rea/pull/3821), [morluto/rea#3820](https://github.com/morluto/rea/issues/3820), [#3799](https://github.com/morluto/rea/pull/3799), [morluto/rea#3798](https://github.com/morluto/rea/issues/3798), [#4344](https://github.com/morluto/rea/pull/4344), [#3856](https://github.com/morluto/rea/pull/3856), [#4166](https://github.com/morluto/rea/pull/4166)). Thanks @gensokyo-dev, @hi2242, @kalayciburak, @kaoru0822-kitauji, @kraken-503, @kukinghan, @N0zoM1z0, @yeseong0412.
@@ -192,7 +192,7 @@ Full contribution record: [571 commits and 236 merged PRs](https://github.com/mo

 ## [6.5.0](https://github.com/morluto/rea/compare/rea-agents-6.4.0...rea-agents-6.5.0) (2026-10-13)

-Provider prerequisites and recorded verification scope are listed in [the testing guide](docs/development/testing.md).
+Provider prerequisites and recorded verification scope are listed in [the testing guide](docs/testing.md).

 ### Highlights

@@ -220,7 +220,7 @@ Provider prerequisites and recorded verification scope are listed in [the testin
 - **HarmonyOS packages:** inventory HAP/HSP/App Pack structures without executing code. The recorded real workflow covers one pinned HAP through repository-built CLI/MCP; installed-package and real HSP/App Pack coverage remain unverified. ([#1447](https://github.com/morluto/rea/pull/1447)). Thanks @BaaRai.
 - **Ghidra raw inputs and references:** compatible Linux/macOS Ghidra profiles accept caller-selected raw architecture/entry information and expose typed incoming references at exact addresses. Windows Ghidra P0 admits the raw NMOS 6502 profile described below; other raw targets and the incoming-reference facet remain outside Windows P0. ([#1868](https://github.com/morluto/rea/pull/1868), [issue morluto/rea#1836](https://github.com/morluto/rea/issues/1836), [#1715](https://github.com/morluto/rea/pull/1715), [issue morluto/rea#1245](https://github.com/morluto/rea/issues/1245)). Thanks @bugstan, @casesolved-co-uk, @mvanhorn, @N0zoM1z0.
 - **Ghidra MIPS:** Add bounded MIPS32r2/o32 relocatable objects, soft-float integer-register storage, admitted MIPS16 shared ELF, and a narrowly admitted recordless legacy MIPS32 executable profile. The latter pins an endian-matched 32-bit language and records inferred o32 as an analysis assumption. Admission follows each documented ABI/flag/relocation boundary. ([#1949](https://github.com/morluto/rea/pull/1949), [issue morluto/rea#1937](https://github.com/morluto/rea/issues/1937), [#1950](https://github.com/morluto/rea/pull/1950), [issue morluto/rea#1938](https://github.com/morluto/rea/issues/1938), [#1991](https://github.com/morluto/rea/pull/1991), [issue morluto/rea#1851](https://github.com/morluto/rea/issues/1851), [#1898](https://github.com/morluto/rea/pull/1898), [issue morluto/rea#1620](https://github.com/morluto/rea/issues/1620)). Thanks @AurelioB, @BaaRai, @bqw371, @kaoru0822-kitauji, @N0zoM1z0.
- **Ghidra RISC-V:** admit little-endian RV32/RV64 `ET_EXEC` ELF declaring the supported double-float ABI. Relocatable/shared, big-endian and other ABI profiles remain refused; see [the profile and recorded lane](docs/providers/ghidra-riscv.md). ([#2151](https://github.com/morluto/rea/pull/2151)). Thanks @NIU-123370.
+- **Ghidra RISC-V:** admit little-endian RV32/RV64 `ET_EXEC` ELF declaring the supported double-float ABI. Relocatable/shared, big-endian and other ABI profiles remain refused; see [the profile and recorded lane](docs/ghidra-riscv.md). ([#2151](https://github.com/morluto/rea/pull/2151)). Thanks @NIU-123370.
 - **PSP static ELF profile:** the Ghidra profile is Linux x64, bounded little-endian ELF32 `ET_EXEC` with the documented PSP/ABI declarations and a compatible caller-installed Allegrex extension. PRX, shared/relocatable images, PBP/ISO/CSO and runtime emulation are outside scope. Historical extension experiments are separate from public-provider verification; real public Ghidra PSP coverage remains unverified. ([#1599](https://github.com/morluto/rea/pull/1599)). Thanks @jaelliot.
 - **Ghidra analysis settings:** apply validated analyzer overrides before analysis while retaining the selected analysis profile. ([#1913](https://github.com/morluto/rea/pull/1913)). Thanks @akushonkamen, @kaoru0822-kitauji, @N0zoM1z0.
 - **Attached native IDA MCP:** add an optional native bridge alongside existing legacy/headless profiles. Recorded native runs use Linux IDA Free 9.4 with a navigation correction and Windows IDA Pro 9.3 with a loopback-listener change; stock native switching, native macOS and Windows IDA Free remain unverified. Attached databases remain read-only and are never saved or closed. ([#1544](https://github.com/morluto/rea/pull/1544)). Thanks @imissapixel, @N0zoM1z0.
@@ -292,7 +292,7 @@ Provider prerequisites and recorded verification scope are listed in [the testin
 - **Source maps:** original-source and mapping rows preserve a null source name when unavailable. Handle null explicitly instead of expecting an invented unknown-source string; new index fields remain optional when reading older Evidence. ([ee50ed1](https://github.com/morluto/rea/commit/ee50ed121e38cc6e1a2ff0dc8b789f15f71c5402)).
 - **Streamed filtered JSON:** `--filter-output` now emits JSON `null` instead of `{}` when the selected value is null; consumers must distinguish a present null from a missing selection. Use `--full-output` when an object envelope is required. ([#2333](https://github.com/morluto/rea/pull/2333)). Thanks @Jackmeson1.
 - **Call graphs:** `get_call_graph.normalized_result` is now `{ graph, limitations }`; read traversal-depth groups under `graph` and retain relationship-specific caveats. Contract/fixture validation does not establish new Ghidra or IDA engine coverage. ([5dfb9d0](https://github.com/morluto/rea/commit/5dfb9d050c2cc44a61b183dae765bef4d22a53b7)).
- **MCP discovery:** `binary_session` no longer repeats `server_identity.catalog.tools`. Use the connected server tool list, grouped `tool_availability` and provider capabilities; see [MCP contracts](docs/reference/mcp-contracts.md). Origin: [6395e8d](https://github.com/morluto/rea/commit/6395e8d3007d5ee453477460e7ee1c51cff76be0). ([#1988](https://github.com/morluto/rea/pull/1988)). Thanks @kaoru0822-kitauji, @N0zoM1z0.
+- **MCP discovery:** `binary_session` no longer repeats `server_identity.catalog.tools`. Use the connected server tool list, grouped `tool_availability` and provider capabilities; see [MCP contracts](docs/mcp-contracts.md). Origin: [6395e8d](https://github.com/morluto/rea/commit/6395e8d3007d5ee453477460e7ee1c51cff76be0). ([#1988](https://github.com/morluto/rea/pull/1988)). Thanks @kaoru0822-kitauji, @N0zoM1z0.

 - **Provider admission:** MIPS targets with unresolved GNU ABI attributes are refused. Supply supported ABI declarations. Saved Hopper databases on macOS are unavailable because the launcher cannot run the analysis bridge when opening a database; select an executable target instead. Database support requires a script-capable database launch route. ([d4bd65c](https://github.com/morluto/rea/commit/d4bd65c53c0254d0195cc7ab8da163dcadfd3b9b)).
 - **Segment extents:** `binary_overview` segment length may be null when Hopper coordinates cannot establish a finite extent in one address space. Preserve unknown rather than converting it to zero or a saturated value. ([36db19c](https://github.com/morluto/rea/commit/36db19c59)).
@@ -372,7 +372,7 @@ Full contribution record: [336 commits and 163 merged PRs](https://github.com/mo

 ### ⚠ BREAKING CHANGES

-* **captures:** Historical captures without current producer accounting or transaction identity, and web diffs missing accessibility or storage dimensions, are rejected. Preserve original captures and recapture with the current producer; update comparison consumers to include every dimension rather than synthesizing missing observations. See the [process capture guide](docs/guides/runtime/process-capture.md) and [browser scenario contract](docs/guides/web/browser-scenario-contract.md). ([3283a45](https://github.com/morluto/rea/commit/3283a45d09457c79e3adadb50a48620926d4bc5b))
+* **captures:** Historical captures without current producer accounting or transaction identity, and web diffs missing accessibility or storage dimensions, are rejected. Preserve original captures and recapture with the current producer; update comparison consumers to include every dimension rather than synthesizing missing observations. See the [process capture guide](docs/process-capture.md) and [browser scenario contract](docs/browser-scenario-contract.md). ([3283a45](https://github.com/morluto/rea/commit/3283a45d09457c79e3adadb50a48620926d4bc5b))
 * **browser:** JSON shape paths now contain typed property and array-element segments. WebMCP input_schema_shape is replaced by input_schema and input_schema_sha256, retaining declared examples and defaults.
 * **process:** Filesystem digest omission entries now require system_code; budget and changed-file omissions use null, and unavailable-file omissions preserve the operating-system error code.
 * **contracts:** Provider analysis outputs must explicitly supply metadata previously repaired with defaults; unsupported nullable facets must be reported as null.
@@ -540,7 +540,7 @@ Full contribution record: [336 commits and 163 merged PRs](https://github.com/mo

 ### ⚠ BREAKING CHANGES

-Read the [6.1 to 6.2 migration guide](docs/migrations/migration-6.2.md) before upgrading. REA's `always-bump-minor` policy includes breaking changes; 6.2 is not a backward-compatibility promise. Preserve original saved files and regenerate missing observations rather than fabricating identities or facts.
+Read the [6.1 to 6.2 migration guide](docs/migration-6.2.md) before upgrading. REA's `always-bump-minor` policy includes breaking changes; 6.2 is not a backward-compatibility promise. Preserve original saved files and regenerate missing observations rather than fabricating identities or facts.

 * **MCP / Evidence / snapshots / artifacts:** Success results are direct canonical Evidence; read `normalized_result` rather than the old `result`/`evidence` wrapper. Evidence requires nullable `analysis_profile`, session provider aliases are removed, snapshots require complete profile-bound query records, and artifact roles/permissions belong to occurrences. Recreate incompatible saved data; adding fields without recomputing their semantic identity is invalid. ([63bf914](https://github.com/morluto/rea/commit/63bf91405cf97b114a84f337fb1272d98a267999))
 * **Process captures:** Legacy v3 conversion is removed. Explicit executable identity and `event_journal` are required; retain old captures and recapture when current comparisons are needed instead of inventing launch identity or event order. ([2a77469](https://github.com/morluto/rea/commit/2a7746998d47446c4db6d4f524e0f183d6803f3f))
@@ -11,7 +11,7 @@ incorrect user instructions warrant standalone corrections. Collect other
 cosmetic-only suggestions in an issue rather than separate PRs.

 For selected architectural owners and dependency paths, use the
-[architecture map](docs/architecture/architecture.mermaid). It is not a complete directory or
+[architecture map](docs/architecture.mermaid). It is not a complete directory or
 import inventory. For current provider wiring, start with
 [`src/composition/binary.ts`](src/composition/binary.ts) for deep candidates and
 the other `src/composition/` factories for tool services, including
@@ -32,7 +32,7 @@ removing it. Preserve validation, lazy loading, caller policy, and resource
 acquisition and cleanup supplied by the old boundary. Published APIs, persisted
 formats, and independently versioned bridges require an explicit compatibility
 decision; an internal representation alone does not establish that obligation.
-See [interpreting boundary facts once](docs/development/tool-design.md#interpret-boundary-facts-once)
+See [interpreting boundary facts once](docs/tool-design.md#interpret-boundary-facts-once)
 for admission ownership and the distinction between repeated validation and
 independent checks.

@@ -44,7 +44,7 @@ Use the [analysis optimization skill](.agents/skills/rea-analysis-optimization/S
 to locate provider and shared-workflow bottlenecks, preserve Evidence, and
 compare equivalent real tasks before claiming an improvement.

-When adding or changing an MCP tool, follow the [tool design guide](docs/development/tool-design.md) and preserve the canonical contracts and generated catalog.
+When adding or changing an MCP tool, follow the [tool design guide](docs/tool-design.md) and preserve the canonical contracts and generated catalog.
 When adding or changing an admission ceiling, budget, or deadline, follow
 [analysis settings, limits, and recovery](docs/design/limits-and-recovery.md)
 for ownership, operation snapshots, provider integration, and the steps for
@@ -234,7 +234,7 @@ guarantee.
 Use the development toolchain pinned in `.nvmrc` and
 `package.json#packageManager`. Run `nvm use` before installing dependencies;
 installed-package runtime support is documented in
-[installation](docs/getting-started/installation.md#start-setup).
+[installation](docs/installation.md#start-setup).
 Use Node.js and npm for source builds and verifier scripts; the installed
 package's Bun runtime support does not extend to those development scripts.

@@ -289,20 +289,16 @@ base revision, or run the suite on Linux or WSL, before attributing them to a
 change. The embedded-artifact parent-swap tests exercise the selected-path
 replacement when the rename succeeds; if Windows refuses it while the admitted
 file is open, they instead verify the refusal and cleanup. See
-[testing](docs/development/testing.md#developer-commands) for command scopes
+[testing](docs/testing.md#developer-commands) for command scopes
 and lane selection.

 `git submodule update --init --recursive` fails at the pinned Unblob submodule
 on Windows and can leave later submodules unchecked out. Apply the
-[Unblob checkout workaround](docs/guides/firmware/firmware-analysis.md#windows-submodule-checkout),
+[Unblob checkout workaround](docs/firmware-analysis.md#windows-submodule-checkout),
 then rerun the command.

 ## Documentation website

-Use the [documentation directory](docs/README.md) and
-[authoring guide](docs/development/documentation.md) for document ownership,
-domain-based feature specifications and architectural decision records.
-
 The VitePress site uses the Markdown files in `docs/`. Run `npm run docs:dev`
 for live editing, `npm run docs:build` to check the production build and
 links, and `npm run docs:preview` to preview that build at `/rea/`.
@@ -356,7 +352,7 @@ npm run check:fast
 `test:local` runs source tests without building. `check:changed` combines cached
 static checks with source tests affected since the merge base with `origin/main`.
 Import-graph selection can miss runtime registration, bridges, and generated data;
-select relevant boundary tests explicitly. See [testing](docs/development/testing.md#developer-commands)
+select relevant boundary tests explicitly. See [testing](docs/testing.md#developer-commands)
 for commands, test placement, pruning, and real-provider prerequisites.

 Before requesting review, run relevant tests and `npm run check`; add
@@ -431,8 +427,8 @@ Run `npm run verify:hopper` on a supported macOS host or
 `npm run verify:hopper:linux` on the supported Linux demo runner. These build
 native fixtures and verify the installed engine through CLI/MCP; package or
 simulated-provider checks do not establish engine behavior. See
-[real-toolchain verification](docs/development/testing.md#end-to-end-integration-and-golden-evidence)
-for prerequisites and scope, and [Hopper setup](docs/getting-started/installation.md#hopper)
+[real-toolchain verification](docs/testing.md#end-to-end-integration-and-golden-evidence)
+for prerequisites and scope, and [Hopper setup](docs/installation.md#hopper)
 for supported hosts and unattended startup.

 Use the default `build/conformance/manifest.json` unless explicitly verifying
@@ -441,7 +437,7 @@ Generated fixtures and manifests remain ignored.

 ## Maintainer release checklist

-Use the [release guide](docs/development/releasing.md). Main pushes automatically refresh a
+Use the [release guide](docs/releasing.md). Main pushes automatically refresh a
 Release Please PR with the next version and changelog. Review its migration
 notes, wait for the current CI checks to pass, and merge it into main to publish.

@@ -10,7 +10,7 @@
 **See a feature you like. Understand how it works, down to the binary level.**

 [![npm version](https://img.shields.io/npm/v/rea-agents?style=flat-square&color=cb3837)](https://www.npmjs.com/package/rea-agents)
-[![MCP tool catalog](https://img.shields.io/badge/MCP-tool_catalog-5c4ee5?style=flat-square)](docs/reference/mcp-contracts.md#generated-catalog)
+[![MCP tool catalog](https://img.shields.io/badge/MCP-tool_catalog-5c4ee5?style=flat-square)](docs/mcp-contracts.md#generated-catalog)
 [![Node.js requirements](https://img.shields.io/badge/Node.js-requirements-339933?style=flat-square&logo=nodedotjs&logoColor=white)](#what-you-can-analyze)
 [![skills.sh](https://skills.sh/b/morluto/rea?style=flat-square)](https://skills.sh/morluto/rea/reverse-engineer-anything)
 [![MIT license](https://img.shields.io/badge/license-MIT-f4c430?style=flat-square)](LICENSE)
@@ -72,7 +72,7 @@ Setup registers REA with your agent and installs matching workflow instructions.

 On Linux, Ghidra, JADX, firmware tool launches and static JavaScript/Electron
 analysis require a procps-compatible `ps` on REA's `PATH` for process ownership
-checks. Recovery steps are in `docs/getting-started/installation.md` under
+checks. Recovery steps are in `docs/installation.md` under
 "Linux owned-process prerequisite".

 ### Set up your agent
@@ -91,8 +91,8 @@ available. Run package acquisition from a trusted directory outside the target
 project. Installation and recovery details are in the setup guide below.

 Setup supports Claude Code, Codex, Cursor, Gemini CLI, Grok Build and
-[other agents](docs/getting-started/installation.md#supported-agents). See
-[installation and setup](docs/getting-started/installation.md) for provider configuration and
+[other agents](docs/installation.md#supported-agents). See
+[installation and setup](docs/installation.md) for provider configuration and
 manual MCP registration and Claude Code/Codex plugin installation.

 MCP uses compact input schemas by default to reduce context overhead. Set
@@ -135,7 +135,7 @@ rea --help
 ```

 For native analysis, configure a provider first. See the
-[CLI and Evidence guide](docs/getting-started/cli.md) for native commands, provider selection,
+[CLI and Evidence guide](docs/cli.md) for native commands, provider selection,
 snapshots and scripting.

 ### Update REA
@@ -191,45 +191,44 @@ CLI commands use the same workflows.
 REA requires Node.js 22.x (>=22.23.4), 24.x (>=24.22.1), or 26.12.1+, plus npm.
 Additional tools and host support depend on the target:

-| Target                  | What REA returns                                                                                  | Requirements and guide                                                                                                                                               |
-| ----------------------- | ------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| Desktop installations   | Runtime candidates, supporting files, component markers and next probes                           | Built-in bounded directory/header inspection; [desktop applications](docs/desktop-applications.md)                                                                   |
-| Native binaries         | Pseudocode, assembly, strings, symbols, calls and references                                      | Hopper, Ghidra, IDA or Kuna; [native analysis](docs/guides/native/native-investigation.md)                                                                           |
-| Offline ELF layout      | Sections, segments, original symbols/relocations and static mitigation candidates                 | Caller-supplied pwntools on Linux x64; [binary diagnostics](docs/guides/native/binary-diagnostics.md)                                                                |
-| Go binaries             | Embedded compiler version, modules, replacements and build settings                               | Built-in static ELF/PE/thin Mach-O inspection; no Go installation required                                                                                           |
-| GPU code objects        | CUDA/HIP targets, selected kernel parameters and resources, retained PTX text                     | Built-in static ELF/PE/fatbin/CUBIN/PTX inspection; [GPU code objects](docs/gpu-code-objects.md)                                                                     |
-| Model artifacts         | GGUF / safetensors metadata, tensor declarations and derived totals                               | Built-in header inspection; optional full-file hash; [model files](docs/model-artifacts.md)                                                                          |
-| IL2CPP metadata         | Unity global-metadata.dat assembly images, type and method names and index ranges                 | Built-in static decoding of versions 24, 27, 29, 31 and 39; no Unity required                                                                                        |
-| Godot PCK               | Archive inventory and extraction, original header/directory facts and selected content identities | Built-in static formats 2, 3 and 4; no Godot required                                                                                                                |
-| Rust binaries           | Embedded cargo-auditable crate names, versions, sources and dependency edges                      | Built-in static ELF/PE/thin Mach-O inspection; [Rust binaries](docs/rust-binaries.md)                                                                                |
-| PE certificates         | Authenticode WIN_CERTIFICATE entries and PKCS#7 signer/X.509 identity fields                      | Built-in static PE inspection; [PE certificates](docs/pe-certificates.md)                                                                                            |
-| PE imports              | Import and delay-load DLL names, ordinals, IAT RVAs and pefile import hash                        | Built-in static PE inspection; [PE imports](docs/pe-imports.md)                                                                                                      |
-| ELF notes               | PT_NOTE/SHT_NOTE owners, types, GNU build-id and ABI-tag fields                                   | Built-in static ELF inspection; [ELF notes](docs/elf-notes.md)                                                                                                       |
-| Binary hardening        | PIE, NX, RELRO, CFG and related header flags for ELF, PE and Mach-O                               | Built-in static header inspection; [binary hardening](docs/binary-hardening.md)                                                                                      |
-| Apple IPS crashes       | .ips metadata, threads, images, registers and documented crash classes                            | Built-in static JSON inspection; [Apple IPS](docs/apple-ips.md)                                                                                                      |
-| Linux kernel modules    | .modinfo keys, __versions CRCs, this_module presence, and signature trailer                       | Built-in static ELF inspection; [kernel modules](docs/kernel-modules.md)                                                                                             |
-| Erlang BEAM             | IFF chunks, atoms, exports, imports, lambdas and the Code header                                  | Built-in static BEAM inspection; [Erlang BEAM](docs/erlang-beam.md)                                                                                                  |
-| WASM artifact           | Validation, sections, exact import/export WAT forms and decoded WAT                               | Caller-supplied WABT 1.0.42; `inspect_wasm_artifact`                                                                                                                 |
-| EVM bytecode            | Dispatch selectors, byte offsets, inferred arguments and mutability                               | Local raw/hex carrier on Linux x64; [offline EVM guide](docs/guides/evm/evm-bytecode.md)                                                                             |
-| SQLite databases        | Tables, columns, indexes, views, triggers and selected ordinary-table rows                        | Local database/WAL snapshot; Node.js 24.x >=24.15 or 26+ with native SQLite limits                                                                                   |
-| Recorded Linux crashes  | Raw notes, every recorded thread's registers/signals and optional mapping candidates              | Caller-supplied pwntools on Linux x64; optional GDB/pwndbg; [recorded crashes](docs/guides/native/recorded-crashes.md)                                               |
-| JavaScript / Electron   | Modules, imports, source maps, routes, IPC and native add-on relationships                        | Node.js and npm; Linux: procps-compatible `ps`; [application analysis](docs/guides/javascript/javascript-application-workflows.md)                                   |
-| Websites                | Page structure, scripts, network observations and requested screenshots                           | A Chrome-family browser; [browser analysis](docs/guides/web/browser-observation.md)                                                                                  |
-| Saved network captures  | Requests, responses, exposed payloads and source locations                                        | HAR or Fiddler Everywhere SAZ; mitmdump on Linux for native mitmproxy; [capture guide](docs/guides/web/web-network-captures.md)                                      |
-| .NET assemblies         | Metadata, CIL instructions, declared native dependencies and build comparisons                    | None (static only); [managed-code guide](docs/guides/managed/managed-code-analysis.md)                                                                               |
-| Android APKs            | Manifest declarations, classes, decompiled methods and references                                 | Headless JADX and a full JDK on Linux/macOS/Windows x64; [Android guide](docs/guides/android/android-analysis.md)                                                    |
-| APK signatures          | v1/v2/v3/v3.1 signers, certificate fingerprints, key rotation and digest self-consistency         | None (static only); `inspect_apk_signature`                                                                                                                          |
-| Android devices         | Devices, packages, processes, logs, dumps, screen captures, and APK/file transfers                | Caller-supplied adb (emulator or hardware); [ADB guide](docs/guides/android/adb-device-analysis.md)                                                                  |
-| JEB projects            | Engine-backed project units, artifact digests and type/method pseudo-code                         | A caller-started JEB client serving MCP, selected with REA_JEB_MCP_URL; [JEB guide](docs/providers/jeb-analysis.md)                                                  |
-| Android resources       | Decoded manifest, string tables, locales and version facts                                        | Caller-supplied Apktool launcher; [resource guide](docs/guides/android/apktool-resource-analysis.md)                                                                 |
-| Flutter apps            | Dart snapshot hash, per-ABI library digests and engine build provenance                           | None (static APK parsing); [Flutter guide](docs/guides/android/flutter-analysis.md)                                                                                  |
-| Firmware                | Regions, extraction results and native-analysis handoffs                                          | Binwalk / Unblob on Linux; [firmware guide](docs/guides/firmware/firmware-analysis.md)                                                                               |
-| Recorded packets        | Selected fields, repeated values, filters and decode-as rules                                     | Linux: TShark 4.x + prlimit; [capture guide](docs/guides/data/packet-captures.md)                                                                                    |
-| Packet summaries        | Endpoints, DNS, TLS SNI, protocol distribution and HTTP requests                                  | Caller-supplied tshark and capinfos (Linux-verified); [pcap guide](docs/guides/data/pcap-analysis.md)                                                                |
-| Recorded logic signals  | Decoder annotations, sample ranges and diagnostics                                                | Linux: sigrok-cli 0.7.2 + prlimit; [signal recordings](docs/guides/signals/signal-recordings.md)                                                                     |
-| Packages and resources  | File inventories, digests, plists, Apple bundle anatomy and extracted resources                   | [Artifact and JavaScript guide](docs/guides/javascript/javascript-artifact-reconstruction.md), [Apple applications](docs/guides/apple/apple-application-analysis.md) |
-| Process behavior        | Terminal output, interactions, exit and filesystem observations, and run comparisons              | Linux/macOS with a native PTY; [process capture](docs/guides/runtime/process-capture.md)                                                                             |
-| PyInstaller executables | CArchive members, Python version, entry scripts and extracted bytecode                            | None (static only); [Python packaged applications](docs/python-packaged-applications.md)                                                                             |
+| Target                  | What REA returns                                                                                  | Requirements and guide                                                                                                                |
+| ----------------------- | ------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------- |
+| Desktop installations   | Runtime candidates, supporting files, component markers and next probes                           | Built-in bounded directory/header inspection; [desktop applications](docs/desktop-applications.md)                                    |
+| Native binaries         | Pseudocode, assembly, strings, symbols, calls and references                                      | Hopper, Ghidra, IDA or Kuna; [native analysis](docs/native-investigation.md)                                                          |
+| Offline ELF layout      | Sections, segments, original symbols/relocations and static mitigation candidates                 | Caller-supplied pwntools on Linux x64; [binary diagnostics](docs/binary-diagnostics.md)                                               |
+| Go binaries             | Embedded compiler version, modules, replacements and build settings                               | Built-in static ELF/PE/thin Mach-O inspection; no Go installation required                                                            |
+| GPU code objects        | CUDA/HIP targets, selected kernel parameters and resources, retained PTX text                     | Built-in static ELF/PE/fatbin/CUBIN/PTX inspection; [GPU code objects](docs/gpu-code-objects.md)                                      |
+| Model artifacts         | GGUF / safetensors metadata, tensor declarations and derived totals                               | Built-in header inspection; optional full-file hash; [model files](docs/model-artifacts.md)                                           |
+| IL2CPP metadata         | Unity global-metadata.dat assembly images, type and method names and index ranges                 | Built-in static decoding of versions 24, 27, 29, 31 and 39; no Unity required                                                         |
+| Godot PCK               | Archive inventory and extraction, original header/directory facts and selected content identities | Built-in static formats 2, 3 and 4; no Godot required                                                                                 |
+| Rust binaries           | Embedded cargo-auditable crate names, versions, sources and dependency edges                      | Built-in static ELF/PE/thin Mach-O inspection; [Rust binaries](docs/rust-binaries.md)                                                 |
+| PE certificates         | Authenticode WIN_CERTIFICATE entries and PKCS#7 signer/X.509 identity fields                      | Built-in static PE inspection; [PE certificates](docs/pe-certificates.md)                                                             |
+| PE imports              | Import and delay-load DLL names, ordinals, IAT RVAs and pefile import hash                        | Built-in static PE inspection; [PE imports](docs/pe-imports.md)                                                                       |
+| ELF notes               | PT_NOTE/SHT_NOTE owners, types, GNU build-id and ABI-tag fields                                   | Built-in static ELF inspection; [ELF notes](docs/elf-notes.md)                                                                        |
+| Apple IPS crashes       | .ips metadata, threads, images, registers and documented crash classes                            | Built-in static JSON inspection; [Apple IPS](docs/apple-ips.md)                                                                       |
+| Linux kernel modules    | .modinfo keys, __versions CRCs, this_module presence, and signature trailer                       | Built-in static ELF inspection; [kernel modules](docs/kernel-modules.md)                                                              |
+| Erlang BEAM             | IFF chunks, atoms, exports, imports, lambdas and the Code header                                  | Built-in static BEAM inspection; [Erlang BEAM](docs/erlang-beam.md)                                                                   |
+| WASM artifact           | Validation, sections, exact import/export WAT forms and decoded WAT                               | Caller-supplied WABT 1.0.42; `inspect_wasm_artifact`                                                                                  |
+| EVM bytecode            | Dispatch selectors, byte offsets, inferred arguments and mutability                               | Local raw/hex carrier on Linux x64; [offline EVM guide](docs/evm-bytecode.md)                                                         |
+| SQLite databases        | Tables, columns, indexes, views, triggers and selected ordinary-table rows                        | Local database/WAL snapshot; Node.js 24.x >=24.15 or 26+ with native SQLite limits                                                    |
+| Recorded Linux crashes  | Raw notes, every recorded thread's registers/signals and optional mapping candidates              | Caller-supplied pwntools on Linux x64; optional GDB/pwndbg; [recorded crashes](docs/recorded-crashes.md)                              |
+| JavaScript / Electron   | Modules, imports, source maps, routes, IPC and native add-on relationships                        | Node.js and npm; Linux: procps-compatible `ps`; [application analysis](docs/javascript-application-workflows.md)                      |
+| Websites                | Page structure, scripts, network observations and requested screenshots                           | A Chrome-family browser; [browser analysis](docs/browser-observation.md)                                                              |
+| Saved network captures  | Requests, responses, exposed payloads and source locations                                        | HAR or Fiddler Everywhere SAZ; mitmdump on Linux for native mitmproxy; [capture guide](docs/web-network-captures.md)                  |
+| .NET assemblies         | Metadata, CIL instructions, declared native dependencies and build comparisons                    | None (static only); [managed-code guide](docs/managed-code-analysis.md)                                                               |
+| Android APKs            | Manifest declarations, classes, decompiled methods and references                                 | Headless JADX and a full JDK on Linux/macOS/Windows x64; [Android guide](docs/android-analysis.md)                                    |
+| APK signatures          | v1/v2/v3/v3.1 signers, certificate fingerprints, key rotation and digest self-consistency         | None (static only); `inspect_apk_signature`                                                                                           |
+| Android devices         | Devices, packages, processes, logs, dumps, screen captures, and APK/file transfers                | Caller-supplied adb (emulator or hardware); [ADB guide](docs/adb-device-analysis.md)                                                  |
+| JEB projects            | Engine-backed project units, artifact digests and type/method pseudo-code                         | A caller-started JEB client serving MCP, selected with REA_JEB_MCP_URL; [JEB guide](docs/jeb-analysis.md)                             |
+| Android resources       | Decoded manifest, string tables, locales and version facts                                        | Caller-supplied Apktool launcher; [resource guide](docs/apktool-resource-analysis.md)                                                 |
+| Flutter apps            | Dart snapshot hash, per-ABI library digests and engine build provenance                           | None (static APK parsing); [Flutter guide](docs/flutter-analysis.md)                                                                  |
+| Firmware                | Regions, extraction results and native-analysis handoffs                                          | Binwalk / Unblob on Linux; [firmware guide](docs/firmware-analysis.md)                                                                |
+| Recorded packets        | Selected fields, repeated values, filters and decode-as rules                                     | Linux: TShark 4.x + prlimit; [capture guide](docs/packet-captures.md)                                                                 |
+| Packet summaries        | Endpoints, DNS, TLS SNI, protocol distribution and HTTP requests                                  | Caller-supplied tshark and capinfos (Linux-verified); [pcap guide](docs/pcap-analysis.md)                                             |
+| Recorded logic signals  | Decoder annotations, sample ranges and diagnostics                                                | Linux: sigrok-cli 0.7.2 + prlimit; [signal recordings](docs/signal-recordings.md)                                                     |
+| Packages and resources  | File inventories, digests, plists, Apple bundle anatomy and extracted resources                   | [Artifact and JavaScript guide](docs/javascript-artifact-reconstruction.md), [Apple applications](docs/apple-application-analysis.md) |
+| Process behavior        | Terminal output, interactions, exit and filesystem observations, and run comparisons              | Linux/macOS with a native PTY; [process capture](docs/process-capture.md)                                                             |
+| PyInstaller executables | CArchive members, Python version, entry scripts and extracted bytecode                            | None (static only); [Python packaged applications](docs/python-packaged-applications.md)                                              |

 Static JavaScript and .NET inspection read the supplied files without running
 the application. Runtime capture runs or interacts with the selected target
@@ -243,15 +242,15 @@ or update either provider.
 <a id="choosing-a-deep-analysis-provider"></a>

 Native formats and host support vary by provider. See
-[Hopper and Ghidra setup](docs/getting-started/installation.md#hopper), the
-[IDA guide](docs/providers/ida-provider.md) (including an optional native MCP bridge), the
+[Hopper and Ghidra setup](docs/installation.md#hopper), the
+[IDA guide](docs/ida-provider.md) (including an optional native MCP bridge), the
 [Kuna decompiler guide](docs/kuna-provider.md), and
-[experimental Windows Ghidra support](docs/providers/windows-ghidra-p0.md).
-Ghidra also supports [16-bit DOS analysis](docs/providers/ghidra-dos.md).
+[experimental Windows Ghidra support](docs/windows-ghidra-p0.md).
+Ghidra also supports [16-bit DOS analysis](docs/ghidra-dos.md).
 For large binaries, raise the provider's startup deadline with
 `REA_GHIDRA_STARTUP_TIMEOUT_MS` or `REA_HOPPER_STARTUP_TIMEOUT_MS`.
-For provider selection, see the [CLI guide](docs/getting-started/cli.md#choose-a-provider).
-Check [release availability](docs/getting-started/installation.md#released-package-and-main)
+For provider selection, see the [CLI guide](docs/cli.md#choose-a-provider).
+Check [release availability](docs/installation.md#released-package-and-main)
 for features added since the latest npm release.

 ## Showcases
@@ -341,8 +340,8 @@ REA exports a runnable environment with a basic test to check that it starts and
 <summary><strong>Which agents can use REA?</strong></summary>

 Any agent that supports local MCP servers. Setup configures the
-[supported agents](docs/getting-started/installation.md#supported-agents); other clients can use
-[manual MCP registration](docs/getting-started/installation.md#mcp-registry).
+[supported agents](docs/installation.md#supported-agents); other clients can use
+[manual MCP registration](docs/installation.md#mcp-registry).

 </details>

@@ -352,7 +351,7 @@ Any agent that supports local MCP servers. Setup configures the
 Deep native analysis uses Hopper, Ghidra, IDA or Kuna, depending on the target
 and operation. Static JavaScript and .NET inspection work without a native
 analysis engine. Setup can install Hopper after approval; Ghidra, IDA and Kuna
-use your existing installations. See [provider setup](docs/getting-started/installation.md#hopper)
+use your existing installations. See [provider setup](docs/installation.md#hopper)
 for the options and their supported targets.

 </details>
@@ -364,7 +363,7 @@ REA starts Hopper when an operation needs it. On macOS, a first-run dialog may
 ask you to choose demo mode or activate your license. Complete that prompt in the
 same user session before your first CLI/MCP operation or unattended job. Open
 Hopper manually if needed. See
-[Hopper startup and troubleshooting](docs/getting-started/installation.md#launcher-paths-and-troubleshooting).
+[Hopper startup and troubleshooting](docs/installation.md#launcher-paths-and-troubleshooting).

 </details>

@@ -373,7 +372,7 @@ Hopper manually if needed. See

 The skill supplies investigation instructions for your agent. Use `npx rea-agents setup`
 to register REA's MCP server and install the matching instructions, then restart
-your agent. See [skill-only installation](docs/getting-started/installation.md#skill-only-installation).
+your agent. See [skill-only installation](docs/installation.md#skill-only-installation).

 </details>

@@ -422,12 +421,12 @@ with your REA version, target type, steps to reproduce and error output.
 Start with the website's [worked guides](https://rea.tools/guides/).
 For exact options, prerequisites and result contracts:

- [Installation and setup](docs/getting-started/installation.md): agent registration, provider configuration, updates and uninstall.
- [Readiness and troubleshooting](docs/getting-started/installation.md#check-readiness-for-your-task): diagnose one agent or analysis engine.
- [CLI and Evidence](docs/getting-started/cli.md): commands, provider selection, snapshots, import/export and exit statuses.
- [MCP contracts](docs/reference/mcp-contracts.md) and [agent prompts](docs/getting-started/mcp-prompts.md): tool results, sessions and guided investigations.
- [Tool catalog](docs/reference/mcp-contracts.md#generated-catalog): generated inventory of tools, providers and CLI commands.
- [Roadmap](docs/development/roadmap.md): planned work and capability trackers.
+- [Installation and setup](docs/installation.md): agent registration, provider configuration, updates and uninstall.
+- [Readiness and troubleshooting](docs/installation.md#check-readiness-for-your-task): diagnose one agent or analysis engine.
+- [CLI and Evidence](docs/cli.md): commands, provider selection, snapshots, import/export and exit statuses.
+- [MCP contracts](docs/mcp-contracts.md) and [agent prompts](docs/mcp-prompts.md): tool results, sessions and guided investigations.
+- [Tool catalog](docs/mcp-contracts.md#generated-catalog): generated inventory of tools, providers and CLI commands.
+- [Roadmap](docs/roadmap.md): planned work and capability trackers.

 Report vulnerabilities through [SECURITY.md](SECURITY.md).

@@ -462,8 +461,8 @@ report a bug or suggest a feature, or [send a pull request](https://github.com/m
 to improve the code or docs.

 See [CONTRIBUTING.md](CONTRIBUTING.md) for development setup and checks,
-[testing](docs/development/testing.md) for verification lanes, and the
-[architecture map](docs/architecture/architecture.mermaid) for selected layers and dependency paths.
+[testing](docs/testing.md) for verification lanes, and the
+[architecture map](docs/architecture.mermaid) for selected layers and dependency paths.

 ## License

@@ -27,7 +27,7 @@ provider-dependent behavior to be reproduced safely.
 REA authenticates its Hopper and Ghidra bridges with per-session random
 capability tokens. POSIX uses current-user Unix sockets; Windows Ghidra uses
 authenticated loopback TCP with a private NTFS runtime whose DACL admits only
-the current user and SYSTEM. See [Windows Ghidra P0](docs/providers/windows-ghidra-p0.md#private-runtime-transport-and-lifecycle).
+the current user and SYSTEM. See [Windows Ghidra P0](docs/windows-ghidra-p0.md#private-runtime-transport-and-lifecycle).
 Tokens are transferred through private session descriptors rather than process
 arguments or environment variables.
 This is not a sandbox and does not protect against malicious processes already
@@ -54,27 +54,27 @@ REA's adapters do not grant, replace, or waive these licenses. The upstream
 executables and their dependency graphs are supplied separately. Git submodules
 pin inspection sources; they are not included in the npm package.

-| Project                        | License and source                                                                                                                                                                                                                                       | REA relationship                                                                                                                                                                                                                                                                                   |
-| ------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| Ghidra                         | [Apache-2.0](https://github.com/NationalSecurityAgency/ghidra/blob/Ghidra_12.1.4_build/LICENSE), with the government-work and component qualifications in its [NOTICE](https://github.com/NationalSecurityAgency/ghidra/blob/Ghidra_12.1.4_build/NOTICE) | Bring your own Ghidra; see [supported versions](docs/getting-started/installation.md#ghidra). Copies of the 12.1.4 [LICENSE](licenses/ghidra-12.1.4-LICENSE.txt), [NOTICE](licenses/ghidra-12.1.4-NOTICE.txt), and [DISCLAIMER](licenses/ghidra-12.1.4-DISCLAIMER.txt) are retained for reference. |
-| ghidra-nativeaot               | [MIT](https://github.com/Washi1337/ghidra-nativeaot/blob/effeb734fc570c32650f88b159608979dc7b423e/LICENSE.md)                                                                                                                                            | Pinned inspection source; derived parser attribution above.                                                                                                                                                                                                                                        |
-| JADX                           | [Apache-2.0](https://github.com/skylot/jadx/blob/v1.5.6/LICENSE)                                                                                                                                                                                         | The audited jadx-headless-mcp source uses JADX 1.5.6 for Android decompilation; the engine JAR is separately supplied.                                                                                                                                                                             |
-| jadx-headless-mcp              | [Apache-2.0](https://github.com/1013503897/jadx-headless-mcp/blob/5844800a486d2248fa949b74c9896285f5b54de2/LICENSE)                                                                                                                                      | v0.7.1; pinned submodule and user-supplied JAR.                                                                                                                                                                                                                                                    |
-| Kuna                           | [Apache-2.0](https://github.com/Noelo-Lab/kuna/blob/v1.990/LICENSE), with its [NOTICE](https://github.com/Noelo-Lab/kuna/blob/v1.990/NOTICE)                                                                                                             | Bring your own `kuna`; REA verified 1.990 and never downloads, installs or bundles it. REA invokes it as a separate process.                                                                                                                                                                       |
-| Apktool                        | [Apache-2.0](https://github.com/iBotPeaches/Apktool/blob/master/LICENSE.md)                                                                                                                                                                              | User-supplied Android resource decoder.                                                                                                                                                                                                                                                            |
-| Binwalk                        | [MIT](https://github.com/ReFirmLabs/binwalk/blob/4fdab3d464d97b68e0af9088df3f9e2e1545b21c/LICENSE)                                                                                                                                                       | v3.1.0; pinned submodule and user-supplied firmware engine.                                                                                                                                                                                                                                        |
-| Unblob                         | [MIT](https://github.com/onekey-sec/unblob/blob/1fcc7a0a584a70a96c31f5a276c20944d199a089/LICENSE)                                                                                                                                                        | 26.6.4; pinned submodule and user-supplied firmware engine.                                                                                                                                                                                                                                        |
-| Wakaru                         | [Apache-2.0](https://github.com/pionxzh/wakaru/blob/8219bf5016a063d7fb215101a8c45d5959ec733f/LICENSE)                                                                                                                                                    | v1.14.0; pinned source and separately obtained JavaScript reconstruction tooling.                                                                                                                                                                                                                  |
-| WABT                           | [Apache-2.0](https://github.com/WebAssembly/wabt/blob/ff0ef7e0009402740c805a9744c09b05be063e48/LICENSE)                                                                                                                                                  | v1.0.42; external WebAssembly tools; [integration provenance](third_party/wabt/README.md).                                                                                                                                                                                                         |
-| pwntools                       | [MIT, with GPL/BSD component qualifications](https://github.com/Gallopsled/pwntools/blob/3ad86ec5adab1abf9781ca7552a6f5d7cff7a33c/LICENSE-pwntools.txt)                                                                                                  | 4.15.0; caller-supplied offline ELF analysis package.                                                                                                                                                                                                                                              |
-| pyelftools                     | [Public-domain dedication and component notices](https://github.com/eliben/pyelftools/blob/v0.33/LICENSE)                                                                                                                                                | 0.33; includes separately licensed bundled material, including Construct.                                                                                                                                                                                                                          |
-| Unicorn                        | [GPL-2.0 and component notices](https://github.com/unicorn-engine/unicorn/blob/2.1.2/COPYING)                                                                                                                                                            | 2.1.2; used by the caller-supplied ELF analysis profile for instruction emulation.                                                                                                                                                                                                                 |
-| pwndbg                         | [MIT](third_party/pwndbg/LICENSE.md)                                                                                                                                                                                                                     | 2026.09.15, commit `55596aa676a2756efb8d67034f31675170eabe48`; separately obtained debugger extension.                                                                                                                                                                                             |
-| GNU GDB                        | [GPL-3.0-or-later](https://sourceware.org/git/?p=binutils-gdb.git;a=blob;f=gdb/COPYING)                                                                                                                                                                  | Caller-supplied debugger for the optional pwndbg core-file workflow.                                                                                                                                                                                                                               |
-| LLDB / LLVM                    | [Apache-2.0 with LLVM exceptions](https://github.com/llvm/llvm-project/blob/main/LICENSE.TXT)                                                                                                                                                            | Caller-supplied debugger; the installed distribution's component and historical notices also apply.                                                                                                                                                                                                |
-| mitmproxy                      | [MIT](https://github.com/mitmproxy/mitmproxy/blob/6c09d56e4c29a92f5ad01b03199977584b8ea14f/LICENSE)                                                                                                                                                      | 12.2.3; separately supplied network capture proxy.                                                                                                                                                                                                                                                 |
-| Android Debug Bridge (adb)     | [Apache-2.0](https://android.googlesource.com/platform/packages/modules/adb/+/refs/heads/main/NOTICE)                                                                                                                                                    | User-supplied Android device tool. A complete Android SDK download has its own [SDK license terms](https://developer.android.com/studio/terms); adb's source license does not replace them.                                                                                                        |
-| ILSpy / ICSharpCode.Decompiler | [MIT](https://github.com/icsharpcode/ILSpy/blob/master/ICSharpCode.Decompiler/Properties/AssemblyInfo.cs)                                                                                                                                                | Optional separately installed .NET decompiler; not a redistributed REA dependency.                                                                                                                                                                                                                 |
+| Project                        | License and source                                                                                                                                                                                                                                       | REA relationship                                                                                                                                                                                                                                                                   |
+| ------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| Ghidra                         | [Apache-2.0](https://github.com/NationalSecurityAgency/ghidra/blob/Ghidra_12.1.4_build/LICENSE), with the government-work and component qualifications in its [NOTICE](https://github.com/NationalSecurityAgency/ghidra/blob/Ghidra_12.1.4_build/NOTICE) | Bring your own Ghidra; see [supported versions](docs/installation.md#ghidra). Copies of the 12.1.4 [LICENSE](licenses/ghidra-12.1.4-LICENSE.txt), [NOTICE](licenses/ghidra-12.1.4-NOTICE.txt), and [DISCLAIMER](licenses/ghidra-12.1.4-DISCLAIMER.txt) are retained for reference. |
+| ghidra-nativeaot               | [MIT](https://github.com/Washi1337/ghidra-nativeaot/blob/effeb734fc570c32650f88b159608979dc7b423e/LICENSE.md)                                                                                                                                            | Pinned inspection source; derived parser attribution above.                                                                                                                                                                                                                        |
+| JADX                           | [Apache-2.0](https://github.com/skylot/jadx/blob/v1.5.6/LICENSE)                                                                                                                                                                                         | The audited jadx-headless-mcp source uses JADX 1.5.6 for Android decompilation; the engine JAR is separately supplied.                                                                                                                                                             |
+| jadx-headless-mcp              | [Apache-2.0](https://github.com/1013503897/jadx-headless-mcp/blob/5844800a486d2248fa949b74c9896285f5b54de2/LICENSE)                                                                                                                                      | v0.7.1; pinned submodule and user-supplied JAR.                                                                                                                                                                                                                                    |
+| Kuna                           | [Apache-2.0](https://github.com/Noelo-Lab/kuna/blob/v1.990/LICENSE), with its [NOTICE](https://github.com/Noelo-Lab/kuna/blob/v1.990/NOTICE)                                                                                                             | Bring your own `kuna`; REA verified 1.990 and never downloads, installs or bundles it. REA invokes it as a separate process.                                                                                                                                                       |
+| Apktool                        | [Apache-2.0](https://github.com/iBotPeaches/Apktool/blob/master/LICENSE.md)                                                                                                                                                                              | User-supplied Android resource decoder.                                                                                                                                                                                                                                            |
+| Binwalk                        | [MIT](https://github.com/ReFirmLabs/binwalk/blob/4fdab3d464d97b68e0af9088df3f9e2e1545b21c/LICENSE)                                                                                                                                                       | v3.1.0; pinned submodule and user-supplied firmware engine.                                                                                                                                                                                                                        |
+| Unblob                         | [MIT](https://github.com/onekey-sec/unblob/blob/1fcc7a0a584a70a96c31f5a276c20944d199a089/LICENSE)                                                                                                                                                        | 26.6.4; pinned submodule and user-supplied firmware engine.                                                                                                                                                                                                                        |
+| Wakaru                         | [Apache-2.0](https://github.com/pionxzh/wakaru/blob/8219bf5016a063d7fb215101a8c45d5959ec733f/LICENSE)                                                                                                                                                    | v1.14.0; pinned source and separately obtained JavaScript reconstruction tooling.                                                                                                                                                                                                  |
+| WABT                           | [Apache-2.0](https://github.com/WebAssembly/wabt/blob/ff0ef7e0009402740c805a9744c09b05be063e48/LICENSE)                                                                                                                                                  | v1.0.42; external WebAssembly tools; [integration provenance](third_party/wabt/README.md).                                                                                                                                                                                         |
+| pwntools                       | [MIT, with GPL/BSD component qualifications](https://github.com/Gallopsled/pwntools/blob/3ad86ec5adab1abf9781ca7552a6f5d7cff7a33c/LICENSE-pwntools.txt)                                                                                                  | 4.15.0; caller-supplied offline ELF analysis package.                                                                                                                                                                                                                              |
+| pyelftools                     | [Public-domain dedication and component notices](https://github.com/eliben/pyelftools/blob/v0.33/LICENSE)                                                                                                                                                | 0.33; includes separately licensed bundled material, including Construct.                                                                                                                                                                                                          |
+| Unicorn                        | [GPL-2.0 and component notices](https://github.com/unicorn-engine/unicorn/blob/2.1.2/COPYING)                                                                                                                                                            | 2.1.2; used by the caller-supplied ELF analysis profile for instruction emulation.                                                                                                                                                                                                 |
+| pwndbg                         | [MIT](third_party/pwndbg/LICENSE.md)                                                                                                                                                                                                                     | 2026.09.15, commit `55596aa676a2756efb8d67034f31675170eabe48`; separately obtained debugger extension.                                                                                                                                                                             |
+| GNU GDB                        | [GPL-3.0-or-later](https://sourceware.org/git/?p=binutils-gdb.git;a=blob;f=gdb/COPYING)                                                                                                                                                                  | Caller-supplied debugger for the optional pwndbg core-file workflow.                                                                                                                                                                                                               |
+| LLDB / LLVM                    | [Apache-2.0 with LLVM exceptions](https://github.com/llvm/llvm-project/blob/main/LICENSE.TXT)                                                                                                                                                            | Caller-supplied debugger; the installed distribution's component and historical notices also apply.                                                                                                                                                                                |
+| mitmproxy                      | [MIT](https://github.com/mitmproxy/mitmproxy/blob/6c09d56e4c29a92f5ad01b03199977584b8ea14f/LICENSE)                                                                                                                                                      | 12.2.3; separately supplied network capture proxy.                                                                                                                                                                                                                                 |
+| Android Debug Bridge (adb)     | [Apache-2.0](https://android.googlesource.com/platform/packages/modules/adb/+/refs/heads/main/NOTICE)                                                                                                                                                    | User-supplied Android device tool. A complete Android SDK download has its own [SDK license terms](https://developer.android.com/studio/terms); adb's source license does not replace them.                                                                                        |
+| ILSpy / ICSharpCode.Decompiler | [MIT](https://github.com/icsharpcode/ILSpy/blob/master/ICSharpCode.Decompiler/Properties/AssemblyInfo.cs)                                                                                                                                                | Optional separately installed .NET decompiler; not a redistributed REA dependency.                                                                                                                                                                                                 |

 Ghidra's original notice credits software developed at the National Security
 Agency. It explains that US-government-created portions are not subject to US
@@ -1,262 +0,0 @@
-"""Run REA inside an agentenv build computer for REA on the host: capture the app, draft its task and export it.
-
-REA sends this file's source through the computer's ``computer-exec/v1`` route as
-``python3 -I -c <source> <command> <JSON arguments>``; each command prints one JSON line and exits. ``start``
-leaves the capture running on its own: its stdin is a FIFO it holds open for reading and writing, so it never
-sees the end of its input, and ``mark`` and ``stop`` write their requests there and wait for the capture's own
-acknowledgement on its progress log. A small shell around the capture writes its exit status to a file, the
-mark a later command reads. REA runs as the session user in the home, with no ``AGENTENV_*`` variable, so
-neither REA nor the app it launches holds the computer's control token, and with ``APT_CONFIG`` naming the
-package lists ``start`` downloads as that user, so the capture finds the package's sources.
-"""
-
-from __future__ import annotations
-
-import hashlib
-import json
-import os
-import re
-import shutil
-import subprocess
-import sys
-import time
-
-POLL_S = 0.2
-TAIL_BYTES = 4096
-
-
-def _say(value: dict) -> int:
-    print(json.dumps(value), flush=True)
-    return 0
-
-
-def _tail(path: str) -> str:
-    try:
-        with open(path, "rb") as handle:
-            handle.seek(max(0, os.path.getsize(path) - TAIL_BYTES))
-            return handle.read().decode("utf-8", "replace")
-    except OSError:
-        return ""
-
-
-def _environment(work: str) -> dict:
-    environment = {name: value for name, value in os.environ.items() if not name.startswith("AGENTENV_")}
-    environment["APT_CONFIG"] = os.path.join(work, "apt", "apt.conf")
-    return environment
-
-
-def _apt(work: str, timeout: float) -> dict:
-    """Download the package lists into the work folder as the session user, until one update succeeds."""
-    root = os.path.join(work, "apt")
-    lists = os.path.join(root, "lists")
-    updated = os.path.join(root, "updated")
-    os.makedirs(os.path.join(lists, "partial"), exist_ok=True)
-    os.makedirs(os.path.join(root, "cache", "archives", "partial"), exist_ok=True)
-    with open(os.path.join(root, "apt.conf"), "w", encoding="utf-8") as conf:
-        conf.write(
-            f'Dir::State::Lists "{lists}";\n'
-            f'Dir::Cache "{root}/cache";\n'
-            'Debug::NoLocking "true";\n'
-            'APT::Update::Error-Mode "any";\n'
-        )
-    # apt keeps lists compressed as it fetched them, such as *_Packages.lz4 on Ubuntu.
-    count = lambda: len([name for name in os.listdir(lists) if re.search(r"_Packages(\.\w+)?$", name)])  # noqa: E731
-    # A marker left by an update that fetched nothing is not a success; download again.
-    if os.path.exists(updated) and count() > 0:
-        return {"lists": count(), "updated": False}
-    log = os.path.join(root, "update.log")
-    try:
-        with open(log, "wb") as output:
-            code = subprocess.run(["apt-get", "update"], env=_environment(work), stdin=subprocess.DEVNULL,
-                                  stdout=output, stderr=subprocess.STDOUT, timeout=timeout).returncode
-    except (OSError, subprocess.TimeoutExpired) as error:
-        return {"lists": count(), "updated": True, "error": f"{type(error).__name__}: {error}"}
-    lists_fetched = count()
-    if code == 0 and lists_fetched > 0:
-        # Only a whole update that fetched lists is kept, so a failed or empty one runs again.
-        open(updated, "w").close()
-        return {"lists": lists_fetched, "updated": True, "exit_code": code}
-    if code == 0:
-        return {"lists": lists_fetched, "updated": True, "exit_code": code,
-                "error": "apt-get update exited 0 without a package list"}
-    return {"lists": lists_fetched, "updated": True, "exit_code": code,
-            "error": f"apt-get update exited {code}: {_tail(log)[-1500:].strip()}"}
-
-
-def _exit_code(capture: str):
-    try:
-        with open(os.path.join(capture, "exit"), encoding="utf-8") as handle:
-            return int(handle.read().strip() or "-1")
-    except (OSError, ValueError):
-        return None
-
-
-def _event_line(path: str, offset: int, kinds: set, name):
-    """The first progress line after ``offset`` whose event is of one of ``kinds``, for ``name`` when given."""
-    try:
-        with open(path, "rb") as handle:
-            handle.seek(offset)
-            lines = handle.read().decode("utf-8", "replace").splitlines()
-    except OSError:
-        return None
-    for line in lines:
-        try:
-            event = json.loads(line)["rea_progress"]["event"]
-        except (ValueError, KeyError, TypeError):
-            continue
-        if isinstance(event, dict) and event.get("kind") in kinds and (name is None or event.get("name") == name):
-            return line
-    return None
-
-
-def _wait(capture: str, offset: int, kinds: set, name, timeout: float) -> dict:
-    """Wait for the capture's event, or for it to exit, or for time to run out."""
-    log = os.path.join(capture, "progress.log")
-    deadline = time.monotonic() + timeout
-    while True:
-        line = _event_line(log, offset, kinds, name)
-        if line is not None:
-            return {"line": line}
-        code = _exit_code(capture)
-        if code is not None:
-            return {"exited": code, "progress": _tail(log), "output": _tail(os.path.join(capture, "capture.out"))}
-        if time.monotonic() > deadline:
-            return {"timed_out": True, "progress": _tail(log)}
-        time.sleep(POLL_S)
-
-
-def start(arguments: dict) -> int:
-    work, capture = os.path.abspath(arguments["work"]), os.path.abspath(arguments["capture"])
-    rea = shutil.which("rea")
-    if rea is None:
-        return _say({"error": "REA is not installed in this computer; start the computer from a request, which installs it."})
-    if os.path.exists(capture):
-        return _say({"error": f"the capture folder {capture} is already used"})
-    apt = _apt(work, arguments.get("apt_timeout_s", 600))
-    try:
-        os.makedirs(capture)
-    except FileExistsError:
-        return _say({"error": f"a stop claimed {capture} before the capture launched", "apt": apt})
-    control = os.path.join(capture, "control")
-    os.mkfifo(control, 0o600)
-    argv = [rea, "capture-desktop-application", "--desktop-entry", arguments["desktop_entry"],
-            "--output", os.path.join(capture, "capture"), "--exclude", work, "--json"]
-    for value in arguments.get("arguments", []):
-        argv += ["--argument", value]
-    if arguments.get("package_file"):
-        argv += ["--package-file", arguments["package_file"]]
-    # Reading and writing, so the capture never reads the end of its input between requests.
-    reader = os.open(control, os.O_RDWR)
-    try:
-        with open(os.path.join(capture, "capture.out"), "wb") as out, \
-                open(os.path.join(capture, "progress.log"), "wb") as progress:
-            process = subprocess.Popen(
-                ["sh", "-c", 'done=$1; shift; "$@"; code=$?; printf "%s" "$code" > "$done.tmp" && mv "$done.tmp" "$done"',
-                 "sh", os.path.join(capture, "exit"), *argv],
-                cwd=os.path.expanduser("~"), env=_environment(work), stdin=reader, stdout=out, stderr=progress,
-                start_new_session=True)
-    finally:
-        os.close(reader)
-    waited = _wait(capture, 0, {"window_open"}, None, arguments.get("timeout_s", 120))
-    return _say({"pid": process.pid, "apt": apt, **waited})
-
-
-def _request(capture: str, line: str) -> bool:
-    """Write one request to the running capture; False when nothing reads its FIFO any more."""
-    try:
-        fd = os.open(os.path.join(capture, "control"), os.O_WRONLY | os.O_NONBLOCK)
-    except OSError:
-        return False
-    try:
-        os.write(fd, (line + "\n").encode("utf-8"))
-    finally:
-        os.close(fd)
-    return True
-
-
-def mark(arguments: dict) -> int:
-    capture, name = os.path.abspath(arguments["capture"]), arguments["name"]
-    code = _exit_code(capture)
-    log = os.path.join(capture, "progress.log")
-    if code is not None:
-        return _say({"exited": code, "progress": _tail(log)})
-    # A checkpoint already taken, whose answer was lost, is answered from the capture's own log.
-    taken = _event_line(log, 0, {"checkpoint"}, name)
-    if taken is not None:
-        return _say({"line": taken})
-    offset = os.path.getsize(log)
-    if not _request(capture, f"checkpoint {name}"):
-        return _say({"error": "the capture is not reading its requests"})
-    return _say(_wait(capture, offset, {"checkpoint", "checkpoint_refused"}, name, arguments.get("timeout_s", 600)))
-
-
-def stop(arguments: dict) -> int:
-    capture = os.path.abspath(arguments["capture"])
-    if _exit_code(capture) is None and not os.path.exists(os.path.join(capture, "control")):
-        # Never launched: claim the folder, so a start still on its way finds it used and launches nothing.
-        os.makedirs(capture, exist_ok=True)
-        return _say({"absent": True})
-    if _exit_code(capture) is None:
-        _request(capture, "stop")
-    deadline = time.monotonic() + arguments.get("timeout_s", 600)
-    while (code := _exit_code(capture)) is None and time.monotonic() < deadline:
-        time.sleep(POLL_S)
-    log = os.path.join(capture, "progress.log")
-    if code is None:
-        return _say({"timed_out": True, "progress": _tail(log)})
-    output = os.path.join(capture, "capture.out")
-    return _say({"exit_code": code, "progress": _tail(log), "output_bytes": os.path.getsize(output)})
-
-
-def run(arguments: dict) -> int:
-    """Run one REA command with its output in a file, after writing the files it reads."""
-    rea = shutil.which("rea")
-    if rea is None:
-        return _say({"error": "REA is not installed in this computer"})
-    for path, text in arguments.get("files", {}).items():
-        os.makedirs(os.path.dirname(path), exist_ok=True)
-        with open(path, "w", encoding="utf-8") as handle:
-            handle.write(text)
-    with open(arguments["stdout"], "wb") as out:
-        try:
-            done = subprocess.run([rea, *arguments["argv"]], cwd=os.path.expanduser("~"),
-                                  env=_environment(os.path.abspath(arguments["work"])), stdin=subprocess.DEVNULL, stdout=out,
-                                  stderr=subprocess.PIPE, timeout=arguments.get("timeout_s", 1800))
-        except subprocess.TimeoutExpired:
-            return _say({"timed_out": True})
-    return _say({"exit_code": done.returncode, "stdout_bytes": os.path.getsize(arguments["stdout"]),
-                 "stderr": done.stderr[-TAIL_BYTES:].decode("utf-8", "replace")})
-
-
-def listing(arguments: dict) -> int:
-    """Every regular file under a folder, by its path relative to the home, with its size and SHA-256.
-
-    The list goes to the file ``output`` names, outside the folder, and the answer gives its size: a large
-    bundle's list outgrows the 1 MiB of stdout a command answers with, so REA reads it through ``data/get``.
-    """
-    home = os.path.expanduser("~")
-    files, skipped = [], []
-    for directory, folders, names in os.walk(os.path.abspath(arguments["root"])):
-        folders.sort()
-        for name in sorted(names):
-            path = os.path.join(directory, name)
-            relative = os.path.relpath(path, home)
-            if os.path.islink(path) or not os.path.isfile(path):
-                skipped.append(relative)
-                continue
-            digest = hashlib.sha256()
-            with open(path, "rb") as handle:
-                for chunk in iter(lambda: handle.read(1 << 20), b""):
-                    digest.update(chunk)
-            files.append({"path": relative, "size": os.path.getsize(path), "sha256": digest.hexdigest()})
-    output = os.path.abspath(arguments["output"])
-    os.makedirs(os.path.dirname(output), exist_ok=True)
-    with open(output, "w", encoding="utf-8") as handle:
-        json.dump({"files": files, "skipped": skipped}, handle)
-    return _say({"listing_bytes": os.path.getsize(output)})
-
-
-COMMANDS = {"start": start, "mark": mark, "stop": stop, "run": run, "list": listing}
-
-if __name__ == "__main__":
-    sys.exit(COMMANDS[sys.argv[1]](json.loads(sys.argv[2])))
@@ -1,83 +0,0 @@
-"""Keep one agentenv computer up for REA until stdin closes or SIGTERM arrives.
-
-REA runs ``computer.py <bundle folder> [task]`` with the agentenv runner's own interpreter, so ``agent_env``
-imports. It deploys the bundle's task, ``smoke`` by default, on this machine with
-``run_bundle(keep=True, emulate=False)``, prints one JSON line naming the computer's address, MCP URL, control
-token and sandbox id, or ``{"error": ...}``, and tears the computer down once its stdin closes or it gets SIGTERM
-or SIGINT. Everything else it or agentenv prints, a build's output included, goes to stderr. It exits 0 once
-the teardown left nothing up, 1 when it did, and 2 when no computer came up.
-"""
-
-from __future__ import annotations
-
-import json
-import os
-import signal
-import sys
-import threading
-
-
-def _protocol():
-    """A private copy of stdout for the JSON line; fd 1 then points at stderr, as do children that inherit it."""
-    protocol = os.fdopen(os.dup(1), "w", encoding="utf-8")
-    os.dup2(2, 1)
-    sys.stdout = sys.stderr
-    return protocol
-
-
-def _say(protocol, value: dict) -> None:
-    protocol.write(json.dumps(value) + "\n")
-    protocol.flush()
-
-
-def _computer(result):
-    """The run's deployed computer, or why there is none."""
-    run = result.runs[0] if result.runs else None
-    if run is None:
-        return None, "the bundle ran no task"
-    if run.error is not None or run.failed_steps:
-        return None, f"the task failed: {run.error or run.failed_steps}"
-    for env in run.context.deployed_envs:
-        if env.environment_url and env.mcp_url and getattr(env, "sandbox_id", None):
-            return env, None
-    return None, "the task deployed no computer"
-
-
-def main(argv: list[str]) -> int:
-    protocol = _protocol()
-    bundle, task = argv[1], argv[2] if len(argv) > 2 else "smoke"
-    try:
-        from agent_env.bundle import run_bundle
-    except ImportError as error:
-        _say(protocol, {"error": f"agent_env does not import with {sys.executable}: {error}"})
-        return 2
-    try:
-        result = run_bundle(bundle, tasks=[task], keep=True, emulate=False, sandbox="local",
-                            on_progress=lambda line: print(line, file=sys.stderr, flush=True))
-    except BaseException as error:  # noqa: BLE001 - a signal's RunInterrupted too; run_bundle tore its runs down
-        _say(protocol, {"error": f"{type(error).__name__}: {error}"})
-        return 2
-    stop = threading.Event()
-    for signum in (signal.SIGTERM, signal.SIGINT):
-        signal.signal(signum, lambda *_: stop.set())
-    env, problem = _computer(result)
-    try:
-        if env is None:
-            _say(protocol, {"error": problem})
-        else:
-            _say(protocol, {"base_url": env.environment_url, "mcp_url": env.mcp_url,
-                            "control_token": env.control_token, "sandbox_id": env.sandbox_id})
-            threading.Thread(target=lambda: (sys.stdin.buffer.read(), stop.set()), daemon=True).start()
-            while not stop.wait(0.5):
-                pass
-    finally:
-        torn_down = result.teardown()
-    still_up = [sandbox for run in torn_down.runs if run.torn_down is not None for sandbox in run.torn_down.still_up]
-    if still_up:
-        print(f"still up after the teardown: {still_up}", file=sys.stderr, flush=True)
-        return 1
-    return 0 if env is not None else 2
-
-
-if __name__ == "__main__":
-    sys.exit(main(sys.argv))
@@ -179,16 +179,12 @@ public final class ReaGhidraBridge extends HeadlessScript {
    private List<FunctionEntry> procedureInventory;
    private List<InventoryItem> stringInventory;
    private DecompInterface decompiler;
-    // A refused Program may only report its admission failure to the client.
-    private String identityAdmissionFailure;
    /** Per-function native decompiler limit from the session; 0 leaves it unbounded. */
    private int decompileTimeoutSeconds;
    // DecompileProcess converts seconds to an int millisecond timer delay.
    private static final int MAX_DECOMPILE_TIMEOUT_SECONDS = Integer.MAX_VALUE / 1000;
    private final ReaGhidraExtensions analysisExtensions = new ReaGhidraExtensions();
    private static AddressSpace sessionDefaultAddressSpace;
-    private Path checkpointDirectory;
-    private long checkpointModification;

    @Override
    public void run() throws Exception {
@@ -197,7 +193,6 @@ public final class ReaGhidraBridge extends HeadlessScript {
            throw new IllegalArgumentException("REA bridge requires one session descriptor");
        }
        Path descriptorPath = Path.of(arguments[0]);
-        checkpointDirectory = descriptorPath.toAbsolutePath().normalize().getParent();
        SessionDescriptor descriptor = readDescriptor(descriptorPath);
        decompileTimeoutSeconds = descriptor.decompileTimeoutSeconds();
        // Windows retains a native immutable bearer descriptor lease until
@@ -229,17 +224,14 @@ public final class ReaGhidraBridge extends HeadlessScript {
            throw new IllegalStateException("Ghidra provider version does not match the session");
        }
        String importedSha256 = currentProgram.getExecutableSHA256();
-        if (importedSha256 == null || !importedSha256.matches("(?i)[0-9a-f]{64}")) {
-            identityAdmissionFailure = "import_identity_unavailable";
-        }
-        else if (!constantTimeEquals(importedSha256.toLowerCase(Locale.ROOT),
-                                     descriptor.targetSha256)) {
-            identityAdmissionFailure = "import_identity_mismatch";
-        }
-        if (identityAdmissionFailure != null) {
-            end(false);
-            serve(descriptor);
-            return;
+        if (importedSha256 == null ||
+            !constantTimeEquals(
+                importedSha256.toLowerCase(Locale.ROOT),
+                descriptor.targetSha256
+            )) {
+            throw new IllegalStateException(
+                "Ghidra imported-byte digest does not match the admitted target"
+            );
        }
        admittedTargetSha256 = descriptor.targetSha256;
        // GhidraScript wraps run() in a transaction. End it before serving so
@@ -250,7 +242,6 @@ public final class ReaGhidraBridge extends HeadlessScript {
                throw new IOException("Windows Ghidra P0 does not admit metadata recovery or database mutation.");
            analysisExtensions.analyze(descriptor.analysisExtensions, currentProgram, monitor);
            initializeDecompiler();
-            checkpointModification = currentProgram.getModificationNumber();
            serve(descriptor);
        }
        finally {
@@ -414,14 +405,6 @@ public final class ReaGhidraBridge extends HeadlessScript {
                    writeSuccess(writer, request.id, result);
                    return;
                }
-                if (identityAdmissionFailure != null) {
-                    // Keep the producer alive until the client has consumed the
-                    // refusal and closed or sent shutdown. Every other request
-                    // remains refused, including further startup attempts.
-                    writeFailure(writer, request.id, identityAdmissionFailure,
-                        "Ghidra imported identity admission failed");
-                    continue;
-                }
                decompileTimeoutSeconds = request.decompileTimeoutSeconds() == null
                    ? descriptor.decompileTimeoutSeconds() : request.decompileTimeoutSeconds();
                writeSuccess(writer, request.id, handleRequest(request, descriptor));
@@ -455,7 +438,6 @@ public final class ReaGhidraBridge extends HeadlessScript {
        if (descriptor.existingProject && isMutatingOperation(request.method))
            throw new RequestFailure("method_unavailable", "Existing Ghidra project sessions are read-only");
        return switch (request.method) {
-            case "checkpoint_program" -> checkpointProgram(request.params, descriptor);
            case "read_binary_inventory_summary" -> binaryInventorySummary(request.params);
            case "inspect_native_load_image" -> inspectNativeLoadImage(request.params);
            case "read_bytes" -> readMemoryBytes(request.params);
@@ -511,31 +493,6 @@ public final class ReaGhidraBridge extends HeadlessScript {
        return method.equals("annotate_native_function") || method.equals("set_address_name") || method.equals("set_addresses_names");
    }

-    /** Internal lifecycle request: the destination is inside this owned runtime. */
-    private JsonObject checkpointProgram(JsonObject params, SessionDescriptor descriptor) throws Exception {
-        requireKeys(params, Set.of("path", "force"));
-        if (descriptor.existingProject || !descriptor.transport.equals("unix-socket"))
-            throw new RequestFailure("method_unavailable", "This Program has no checkpoint authority");
-        Path output = Path.of(requireString(params, "path")).toAbsolutePath().normalize();
-        if (!output.getParent().equals(checkpointDirectory) ||
-            !output.getFileName().toString().matches("checkpoint-[a-f0-9-]{36}\\.gzf"))
-            throw new RequestFailure("invalid_request", "Checkpoint destination must belong to this runtime");
-        JsonElement forced = params.get("force");
-        if (!forced.isJsonPrimitive() || !forced.getAsJsonPrimitive().isBoolean())
-            throw new RequestFailure("invalid_request", "Checkpoint force must be a boolean");
-        boolean force = forced.getAsBoolean();
-        JsonObject result = new JsonObject();
-        boolean changed = currentProgram.getModificationNumber() != checkpointModification;
-        result.addProperty("saved", force || changed);
-        if (force || changed) {
-            if (Files.exists(output)) throw new RequestFailure("invalid_request", "Checkpoint destination already exists");
-            currentProgram.saveToPackedFile(output.toFile(), monitor);
-            checkpointModification = currentProgram.getModificationNumber();
-            result.addProperty("path", output.toString());
-        }
-        return result;
-    }
-
    private JsonObject sessionInfo(SessionDescriptor descriptor) throws Exception {
        boolean timedOut = analysisTimeoutOccurred();
        JsonObject provider = new JsonObject();
@@ -814,8 +771,6 @@ public final class ReaGhidraBridge extends HeadlessScript {
        return result;
    }

-    private record ByteSearchBlock(MemoryBlock block, Address low, Address high) {}
-
    private JsonObject searchMemoryBytes(JsonObject params, SessionDescriptor descriptor) throws Exception {
        // mask, start, end, and cursor are omitted when absent; JSON encoding drops those keys.
        Set<String> keys = params.keySet();
@@ -876,13 +831,16 @@ public final class ReaGhidraBridge extends HeadlessScript {
        JsonArray blocks = new JsonArray();
        JsonArray skipped = new JsonArray();
        JsonArray notLoaded = new JsonArray();
-        List<ByteSearchBlock> eligible = new ArrayList<>();
+        long covered = 0;
+        String next = null;
        for (MemoryBlock block : ordered) {
            monitor.checkCancelled();
            Address low = block.getStart();
            Address high = block.getEnd();
            Address bound = start == null ? end : start;
            if (bound != null && !bound.getAddressSpace().equals(low.getAddressSpace())) continue;
+            // Without bounds, search loaded memory only. Non-loaded file parts
+            // (such as .symtab) and overlays stay reachable through explicit bounds.
            if (bound == null && (!block.isLoaded() || block.isOverlay())) {
                notLoaded.add(byteSearchCoverage(block, low, high));
                continue;
@@ -894,66 +852,40 @@ public final class ReaGhidraBridge extends HeadlessScript {
                skipped.add(byteSearchCoverage(block, low, high));
                continue;
            }
-            eligible.add(new ByteSearchBlock(block, low, high));
-        }
-        long covered = 0;
-        String next = null;
-        for (int first = 0; first < eligible.size() && next == null;) {
-            monitor.checkCancelled();
-            int last = first;
-            while (last + 1 < eligible.size()) {
-                monitor.checkCancelled();
-                ByteSearchBlock previous = eligible.get(last);
-                ByteSearchBlock following = eligible.get(last + 1);
-                if (!previous.high().getAddressSpace().equals(following.low().getAddressSpace()) ||
-                    previous.high().next() == null || !previous.high().next().equals(following.low())) break;
-                last++;
-            }
-            Address low = eligible.get(first).low();
-            Address high = eligible.get(last).high();
+            if (next != null) continue;
            if (resume != null && low.compareTo(resume) < 0) low = resume;
-            if (low.compareTo(high) <= 0 && low.getAddressSpace().equals(high.getAddressSpace())) {
-                Address at = low;
-                Address examinedEnd = high;
-                while (at != null && at.compareTo(high) <= 0 && high.subtract(at) >= bytes.length - 1L) {
-                    monitor.checkCancelled();
-                    // findBytes bounds candidate starts. The entire candidate remains in this eligible run.
-                    Address found = currentProgram.getMemory().findBytes(at, high.subtract(bytes.length - 1L), bytes, masks, true, monitor);
-                    monitor.checkCancelled();
-                    if (found == null || high.subtract(found) < bytes.length - 1L) break;
-                    if (matches.size() == limit) {
-                        next = binding + ":" + canonicalAddress(found);
-                        examinedEnd = found.addNoWrap(bytes.length - 1L);
-                        break;
-                    }
-                    MemoryBlock matchBlock = currentProgram.getMemory().getBlock(found);
-                    JsonObject match = new JsonObject();
-                    match.addProperty("address", canonicalAddress(found));
-                    match.addProperty("segment", matchBlock.getName());
-                    Long offset = targetFileOffset(matchBlock, found).offset();
-                    match.add("file_offset", offset == null ? JsonNull.INSTANCE : GSON.toJsonTree(offset));
-                    Function function = currentProgram.getFunctionManager().getFunctionContaining(found);
-                    JsonObject procedure = new JsonObject();
-                    if (function != null) {
-                        procedure.addProperty("address", canonicalAddress(function.getEntryPoint()));
-                        procedure.addProperty("name", function.getName(true));
-                    }
-                    match.add("procedure", function == null ? JsonNull.INSTANCE : procedure);
-                    matches.add(match);
-                    at = found.next();
+            if (low.compareTo(high) > 0 || !low.getAddressSpace().equals(high.getAddressSpace())) continue;
+            Address at = low;
+            Address examinedEnd = high;
+            while (at != null && at.compareTo(high) <= 0 && high.subtract(at) >= bytes.length - 1L) {
+                monitor.checkCancelled();
+                // Ghidra's end address bounds candidate starts, not the final matched byte.
+                Address found = currentProgram.getMemory().findBytes(at, high.subtract(bytes.length - 1L), bytes, masks, true, monitor);
+                monitor.checkCancelled();
+                if (found == null || high.subtract(found) < bytes.length - 1L) break;
+                if (matches.size() == limit) {
+                    next = binding + ":" + canonicalAddress(found);
+                    examinedEnd = found.addNoWrap(bytes.length - 1L);
+                    break;
                }
-                for (int index = first; index <= last; index++) {
-                    monitor.checkCancelled();
-                    ByteSearchBlock item = eligible.get(index);
-                    Address coveredLow = item.low().compareTo(low) < 0 ? low : item.low();
-                    Address coveredHigh = item.high().compareTo(examinedEnd) > 0 ? examinedEnd : item.high();
-                    if (coveredLow.compareTo(coveredHigh) > 0) continue;
-                    JsonObject coverage = byteSearchCoverage(item.block(), coveredLow, coveredHigh);
-                    covered = Math.addExact(covered, coverage.get("bytes").getAsLong());
-                    blocks.add(coverage);
+                JsonObject match = new JsonObject();
+                match.addProperty("address", canonicalAddress(found));
+                match.addProperty("segment", block.getName());
+                Long offset = targetFileOffset(block, found).offset();
+                match.add("file_offset", offset == null ? JsonNull.INSTANCE : GSON.toJsonTree(offset));
+                Function function = currentProgram.getFunctionManager().getFunctionContaining(found);
+                JsonObject procedure = new JsonObject();
+                if (function != null) {
+                    procedure.addProperty("address", canonicalAddress(function.getEntryPoint()));
+                    procedure.addProperty("name", function.getName(true));
                }
+                match.add("procedure", function == null ? JsonNull.INSTANCE : procedure);
+                matches.add(match);
+                at = found.next();
            }
-            first = last + 1;
+            JsonObject coverage = byteSearchCoverage(block, low, examinedEnd);
+            covered = Math.addExact(covered, coverage.get("bytes").getAsLong());
+            blocks.add(coverage);
        }
        JsonObject searched = new JsonObject();
        searched.add("blocks", blocks);
@@ -1078,7 +1010,7 @@ public final class ReaGhidraBridge extends HeadlessScript {
            } catch (RequestFailure failure) {
                // Existing names/addresses win. Only an unresolved numeric input
                // can fall back to source coordinates; ambiguity never falls back.
-                if (!failure.code.equals("procedure_not_found") || !selector.matches("0x[0-9a-fA-F]+"))
+                if (!failure.code.equals("not_found") || !selector.matches("0x[0-9a-fA-F]+"))
                    throw failure;
            }
        }
@@ -1105,17 +1037,17 @@ public final class ReaGhidraBridge extends HeadlessScript {
        }
        List<Address> candidates = new ArrayList<>(mappedAddresses);
        if (candidates.size() > 1)
-            throw new RequestFailure("file_offset_ambiguous", "File offset " + coordinate +
+            throw new RequestFailure("ambiguous", "File offset " + coordinate +
                " has multiple loaded mappings: " + candidates.stream().map(ReaGhidraBridge::canonicalAddress).toList() +
                "; select an explicit analysis address");
        if (candidates.isEmpty())
-            throw new RequestFailure("file_offset_unmapped", "File offset " + coordinate +
+            throw new RequestFailure("not_found", "File offset " + coordinate +
                " has no loaded source mapping for the admitted target file; Ghidra image base: " + canonicalAddress(currentProgram.getImageBase()) +
                ". Inspect mappings with rea inspect-native-load-image <path> --provider ghidra --json or MCP inspect_native_load_image.");
        Address mapped = candidates.get(0);
        Function function = functionAtOrContaining(mapped);
        if (function == null)
-            throw new RequestFailure("procedure_not_found", "File offset " + coordinate +
+            throw new RequestFailure("not_found", "File offset " + coordinate +
                " maps to analysis address " + canonicalAddress(mapped) +
                ", but no procedure starts at or contains that address in the current Ghidra analysis. " +
                "Choose an observed procedure with CLI rea search <path> . --kind procedures --mode regex --provider ghidra --json or MCP list_procedures.");
@@ -1318,12 +1250,6 @@ public final class ReaGhidraBridge extends HeadlessScript {
                    if (component.getDataType() instanceof ghidra.program.model.data.BitFieldDataType bitfield) {
                        field.addProperty("bit_size", bitfield.getBitSize());
                        field.addProperty("bit_offset", bitfield.getBitOffset());
-                        JsonObject bitField = new JsonObject();
-                        bitField.addProperty("base_type_id", bitfield.getBaseDataType().getPathName());
-                        bitField.addProperty("declared_bit_size", bitfield.getDeclaredBitSize());
-                        bitField.addProperty("component_type_lookup", typeLookupResult(bitfield));
-                        bitField.addProperty("base_type_lookup", typeLookupResult(bitfield.getBaseDataType()));
-                        field.add("bit_field", bitField);
                    }
                    field.addProperty("status", "observed");
                    field.addProperty("flexible_tail", "unknown");
@@ -1354,7 +1280,7 @@ public final class ReaGhidraBridge extends HeadlessScript {
        result.add("members", members);
        result.addProperty("total_fields", totalFields);
        result.addProperty("truncated", totalFields > 20_000);
-        result.add("limitations", GSON.toJsonTree(List.of("Layouts are Ghidra data-type database observations; original debug/source authority and flexible-tail semantics are not inferred. Component type paths do not necessarily identify separately registered types; bit-field lookups report whether the manager resolves equivalent types.", "At most 20000 fields or enum members are serialized per type to bound provider output. total_fields and truncated report omissions. Enum values preserve Ghidra's signed long representation.")));
+        result.add("limitations", GSON.toJsonTree(List.of("Layouts are Ghidra data-type database observations; original debug/source authority and flexible-tail semantics are not inferred. Nested and recursive types retain category-path identities for separate inspection.", "At most 20000 fields or enum members are serialized per type to bound provider output. total_fields and truncated report omissions. Enum values preserve Ghidra's signed long representation.")));
        if (type != null) {
            JsonObject metadata = analysisExtensions.inspectDataType(currentProgram, type, address, monitor);
            if (metadata != null) result.add("metadata_recovery", metadata);
@@ -1362,11 +1288,6 @@ public final class ReaGhidraBridge extends HeadlessScript {
        return result;
    }

-    private String typeLookupResult(DataType type) {
-        DataType resolved = currentProgram.getDataTypeManager().getDataType(type.getPathName());
-        return resolved == null ? "not-found" : resolved.isEquivalent(type) ? "equivalent" : "different";
-    }
-
    private JsonObject instructionReference(Reference reference) {
        JsonObject item = new JsonObject();
        JsonObject kind = referenceKind(reference);
@@ -1414,29 +1335,8 @@ public final class ReaGhidraBridge extends HeadlessScript {
        flow.addProperty("conditional", false);
        flow.addProperty("computed", false);
        if (instruction == null) {
-            Instruction containing = currentProgram.getListing().getInstructionContaining(address);
-            boolean inMemory = currentProgram.getMemory().contains(address);
-            Data containingData = inMemory && containing == null
-                ? currentProgram.getListing().getDefinedDataContaining(address) : null;
-            result.addProperty("status", !inMemory ? "outside-memory" : containing != null
-                ? "not-instruction-boundary" : containingData != null ? "data" : "not-in-listing");
-            if (inMemory && containing == null && containingData != null) {
-                JsonObject parentData = new JsonObject();
-                parentData.addProperty("address", canonicalAddress(containingData.getAddress()));
-                parentData.addProperty("length", containingData.getLength());
-                parentData.addProperty("type_id", containingData.getDataType().getPathName());
-                parentData.addProperty("provenance", "ghidra-listing");
-                result.add("containing_data", parentData);
-            }
-            if (containing != null && currentProgram.getMemory().contains(address)) {
-                JsonObject containingInstruction = new JsonObject();
-                containingInstruction.addProperty("address", canonicalAddress(containing.getAddress()));
-                containingInstruction.addProperty("length", containing.getLength());
-                containingInstruction.addProperty("mnemonic", containing.getMnemonicString());
-                containingInstruction.addProperty("raw_disassembly", containing.toString());
-                containingInstruction.addProperty("provenance", "ghidra-listing");
-                result.add("containing_instruction", containingInstruction);
-            }
+            result.addProperty("status", !currentProgram.getMemory().contains(address) ? "outside-memory" : currentProgram.getListing().getInstructionContaining(address) != null
+                ? "not-instruction-boundary" : currentProgram.getListing().getDefinedDataContaining(address) != null ? "data" : "not-in-listing");
            for (String key : List.of("bytes", "length", "mnemonic", "raw_disassembly")) result.add(key, JsonNull.INSTANCE);
        } else {
            result.addProperty("status", "decoded");
@@ -1951,9 +1851,6 @@ public final class ReaGhidraBridge extends HeadlessScript {
        limitations.add(
            "Def-use links do not cross function boundaries and may omit memory aliasing, call side effects, or unresolved indirect flow."
        );
-        limitations.add(
-            "Memory read/write effects cover high-p-code LOAD and STORE operations only; direct memory address varnodes in other operations are not included. An empty effect list does not establish that no memory is accessed. Recorded instruction references may provide complementary evidence."
-        );
        limitations.add(
            "Memory read/write effects include stack and temporary memory operations; they do not identify persistent state or business meaning."
        );
@@ -2400,7 +2297,7 @@ public final class ReaGhidraBridge extends HeadlessScript {
                if (!match.matched()) {
                    continue;
                }
-                JsonObject item = resultItem(entry.item, "procedure");
+                JsonObject item = resultItem(entry.item, null);
                if (!match.aliases().isEmpty()) {
                    JsonArray aliases = new JsonArray();
                    for (String alias : match.aliases()) aliases.add(alias);
@@ -2415,7 +2312,7 @@ public final class ReaGhidraBridge extends HeadlessScript {
            if (!matcher.matches(item.value)) {
                continue;
            }
-            items.add(resultItem(item, procedureSearch ? "procedure" : "string"));
+            items.add(resultItem(item, null));
        }
        return items;
    }
@@ -2561,7 +2458,7 @@ public final class ReaGhidraBridge extends HeadlessScript {
                if (matchProcedureNames(entry, selector).matched()) matches.add(entry.function);
            }
            if (matches.size() > 1)
-                throw new RequestFailure("procedure_ambiguous", "Ghidra procedure name is ambiguous: " + value +
+                throw new RequestFailure("ambiguous", "Ghidra procedure name is ambiguous: " + value +
                    "; select an exact entry address from " + matches.stream()
                        .map(function -> canonicalAddress(function.getEntryPoint())).toList());
            if (matches.size() == 1) return matches.get(0);
@@ -2569,11 +2466,11 @@ public final class ReaGhidraBridge extends HeadlessScript {
        // Retain legacy bare-hex address input only when no symbol matches.
        Address address = explicitAddress ? parseReaAddress(value) : tryParseAddress(value);
        if (address == null)
-            throw new RequestFailure("procedure_not_found", "Unknown Ghidra procedure name or address: " + value);
+            throw new RequestFailure("not_found", "Unknown Ghidra procedure name or address: " + value);
        Function function = functionAtOrContaining(address);
        if (function == null)
            // Other procedure operations retain their analysis-address semantics.
-            throw new RequestFailure("procedure_not_found", "No procedure exists at the requested address: " + value +
+            throw new RequestFailure("not_found", "No procedure exists at the requested address: " + value +
                "; Ghidra image base: " + canonicalAddress(currentProgram.getImageBase()) +
                ". Choose an observed analysis address. CLI: rea search <path> . --kind procedures --mode regex --provider ghidra --json; " +
                "MCP: list_procedures. Inspect the loaded base and source mappings with CLI rea analyze <path> --provider ghidra --json " +
@@ -5019,7 +4916,7 @@ public final class ReaGhidraBridge extends HeadlessScript {
            // without retaining its cause. This producer reason is not bad syntax.
            if (exception.getDescription().equals("Stack overflow during pattern compilation"))
                throw regexStackExhausted(expression, "compiling");
-            throw new RequestFailure("invalid_regex_pattern", "Invalid regex pattern " + expression + ": " + exception.getDescription() + " at index " + exception.getIndex());
+            throw new RequestFailure("invalid_request", "Invalid regex pattern " + expression + ": " + exception.getDescription() + " at index " + exception.getIndex());
        }
        catch (StackOverflowError exhausted) {
            throw regexStackExhausted(expression, "compiling");
@@ -37,7 +37,7 @@ import org.xml.sax.InputSource;
 /**
 * Apply the committed RISC-V calling-convention policy after analysis. Ghidra's generic RV32
 * compiler specification models ilp32d. Each policy derives a program-specific prototype from the
- * program's own default prototype, as its {@link Policy} row and docs/providers/ghidra-riscv.md state. The
+ * program's own default prototype, as its {@link Policy} row and docs/ghidra-riscv.md state. The
 * script installs the prototype as a specification extension and assigns it, with dynamic
 * storage, to every non-thunk function, external function and function definition.
 */
@@ -26,6 +26,7 @@ ARGUMENT_REGISTERS = {
    "x86_64h": ["rdi", "rsi", "rdx", "rcx", "r8", "r9"],
 }
 MAX_SELECTOR_BYTES = 1024
+MAX_REPORTED_LOCATIONS = 64
 MAX_OTHER_STOPS = 256
 MAX_TRACE_BYTES = 8 * 1024 * 1024
 MAX_TRACE_FRAMES = 65_536
@@ -243,20 +244,6 @@ def _hex(value):
    return "0x%x" % value


-def _source_location(address):
-    """Preserve available line-entry facets without acquiring source files."""
-    entry = address.GetLineEntry()
-    if not entry.IsValid():
-        return None
-    file_spec = entry.GetFileSpec()
-    file_path = str(file_spec) if file_spec.IsValid() else None
-    line = entry.GetLine() or None
-    column = entry.GetColumn() or None
-    if not file_path and line is None and column is None:
-        return None
-    return {"file_path": file_path or None, "line": line, "column": column}
-
-
 def _location(address, target):
    """Load and file address, module and symbol of one code address."""
    module = address.GetModule()
@@ -270,7 +257,6 @@ def _location(address, target):
        "module": module.GetFileSpec().GetFilename() if module.IsValid() else None,
        "module_path": str(module.GetFileSpec()) if module.IsValid() else None,
        "symbol": symbol.GetName() if symbol.IsValid() else None,
-        "source_location": _source_location(address),
    }
    return location

@@ -519,19 +505,20 @@ def _breakpoint_report(target, created, config):
                if not _wanted(config["breakpoints"][index], location["symbol"] or ""):
                    continue
                count += 1
-                remaining_bytes = (
-                    MAX_BREAKPOINT_LOCATION_BYTES - retained_location_bytes
-                )
-                if not _fits_trace_budget(location, remaining_bytes):
-                    locations_truncated = True
-                    continue
-                location_bytes = len(json.dumps(location).encode("utf-8"))
-                addition = location_bytes + (1 if locations else 0)
-                if addition > remaining_bytes:
-                    locations_truncated = True
-                    continue
-                locations.append(location)
-                retained_location_bytes += addition
+                if len(locations) < MAX_REPORTED_LOCATIONS:
+                    remaining_bytes = (
+                        MAX_BREAKPOINT_LOCATION_BYTES - retained_location_bytes
+                    )
+                    if not _fits_trace_budget(location, remaining_bytes):
+                        locations_truncated = True
+                        continue
+                    location_bytes = len(json.dumps(location).encode("utf-8"))
+                    addition = location_bytes + (1 if locations else 0)
+                    if addition > remaining_bytes:
+                        locations_truncated = True
+                        continue
+                    locations.append(location)
+                    retained_location_bytes += addition
        report.append({"index": index, "location_count": count, "locations": locations})
    return report, locations_truncated

@@ -25,45 +25,6 @@ spec.loader.exec_module(tracer)


 class NativeTraceBudgetTests(unittest.TestCase):
-    def test_source_coordinates_preserve_partial_metadata_without_reading_source(self):
-        def address(valid=True, file_valid=True, line=23, column=7):
-            class SourceFileSpec:
-                def IsValid(self):
-                    return file_valid
-
-                def __str__(self):
-                    return "/missing/é space/fixture.pas"
-
-            file_spec = SourceFileSpec()
-            entry = types.SimpleNamespace(
-                IsValid=lambda: valid,
-                GetFileSpec=lambda: file_spec,
-                GetLine=lambda: line,
-                GetColumn=lambda: column,
-            )
-            return types.SimpleNamespace(GetLineEntry=lambda: entry)
-
-        self.assertEqual(
-            tracer._source_location(address()),
-            {"file_path": "/missing/é space/fixture.pas", "line": 23, "column": 7},
-        )
-        self.assertEqual(
-            tracer._source_location(address(column=0)),
-            {"file_path": "/missing/é space/fixture.pas", "line": 23, "column": None},
-        )
-        self.assertEqual(
-            tracer._source_location(address(file_valid=False)),
-            {"file_path": None, "line": 23, "column": 7},
-        )
-        self.assertEqual(
-            tracer._source_location(address(line=0)),
-            {"file_path": "/missing/é space/fixture.pas", "line": None, "column": 7},
-        )
-        self.assertIsNone(tracer._source_location(address(valid=False)))
-        self.assertIsNone(
-            tracer._source_location(address(file_valid=False, line=0, column=0))
-        )
-
    def test_invalid_launch_process_reports_explicit_no_creation(self):
        class InvalidProcess:
            def IsValid(self):
@@ -429,9 +390,6 @@ class NativeTraceBudgetTests(unittest.TestCase):
                return FileSpec()

        class Address:
-            def GetLineEntry(self):
-                return types.SimpleNamespace(IsValid=lambda: False)
-
            def GetModule(self):
                return Module()

@@ -472,34 +430,6 @@ class NativeTraceBudgetTests(unittest.TestCase):
        self.assertEqual(report[0]["locations"], [])
        self.assertFalse(locations_truncated)

-    def test_breakpoint_report_keeps_all_locations_under_aggregate_budget(self):
-        class Location:
-            def __init__(self, index):
-                self.index = index
-
-            def GetAddress(self):
-                return self.index
-
-        class Breakpoint:
-            def GetNumLocations(self):
-                return 65
-
-            def GetLocationAtIndex(self, index):
-                return Location(index)
-
-        with patch.object(
-            tracer,
-            "_location",
-            side_effect=lambda address, _target: {"address": address, "symbol": None},
-        ), patch.object(tracer, "_wanted", return_value=True):
-            report, locations_truncated = tracer._breakpoint_report(
-                object(), [[Breakpoint()]], {"breakpoints": [{}]}
-            )
-
-        self.assertEqual(report[0]["location_count"], 65)
-        self.assertEqual(len(report[0]["locations"]), 65)
-        self.assertFalse(locations_truncated)
-
    def test_breakpoint_report_bounds_aggregate_location_json(self):
        tracer.lldb.LLDB_INVALID_ADDRESS = -1
        symbol_name = (
@@ -533,24 +463,7 @@ class NativeTraceBudgetTests(unittest.TestCase):
            def GetFileSpec(self):
                return FileSpec()

-        class SourceFileSpec:
-            def IsValid(self):
-                return True
-
-            def __str__(self):
-                return source_path
-
        class Address:
-            def GetLineEntry(self):
-                if source_path is None:
-                    return types.SimpleNamespace(IsValid=lambda: False)
-                return types.SimpleNamespace(
-                    IsValid=lambda: True,
-                    GetFileSpec=SourceFileSpec,
-                    GetLine=lambda: 15,
-                    GetColumn=lambda: 3,
-                )
-
            def GetModule(self):
                return Module()

@@ -577,35 +490,19 @@ class NativeTraceBudgetTests(unittest.TestCase):
        breakpoint_count = 1000
        created = [[Breakpoint()] for _ in range(breakpoint_count)]
        config = {"breakpoints": [{"kind": "objc-method"}] * breakpoint_count}
-        for source_path in (None, "/tmp/" + "源🚀" * 3000 + "/calls.pas"):
-            with self.subTest(source_path_present=source_path is not None):
-                report, locations_truncated = tracer._breakpoint_report(
-                    object(), created, config
-                )
-                retained_bytes = sum(
-                    len(json.dumps(location).encode("utf-8"))
-                    + (1 if index > 0 else 0)
-                    for row in report
-                    for index, location in enumerate(row["locations"])
-                )
-                self.assertTrue(locations_truncated)
-                self.assertEqual(
-                    sum(row["location_count"] for row in report), 64_000
-                )
-                self.assertLess(
-                    sum(len(row["locations"]) for row in report), 64_000
-                )
-                self.assertLessEqual(
-                    retained_bytes, tracer.MAX_BREAKPOINT_LOCATION_BYTES
-                )
-                if source_path is not None:
-                    self.assertTrue(
-                        any(
-                            location["source_location"]["file_path"] == source_path
-                            for row in report
-                            for location in row["locations"]
-                        )
-                    )
+        report, locations_truncated = tracer._breakpoint_report(
+            object(), created, config
+        )
+        retained_bytes = sum(
+            len(json.dumps(location).encode("utf-8"))
+            + (1 if index > 0 else 0)
+            for row in report
+            for index, location in enumerate(row["locations"])
+        )
+        self.assertTrue(locations_truncated)
+        self.assertEqual(sum(row["location_count"] for row in report), 64_000)
+        self.assertLess(sum(len(row["locations"]) for row in report), 64_000)
+        self.assertLessEqual(retained_bytes, tracer.MAX_BREAKPOINT_LOCATION_BYTES)


 if __name__ == "__main__":
@@ -109,7 +109,7 @@ class CoreContextTests(unittest.TestCase):
        self.assertFalse(result["ok"])
        self.assertEqual(result["reason"], "output-limit")
        self.assertNotIn("exceeds64", result["message"])
-        self.assertIn("64 MiB", result["message"])
+        self.assertEqual(result["message"], "Complete debugger context exceeds the 64 MiB reply budget.")
        self.assertEqual(reads, [])
        self.assertEqual(queries, ["maps"])

@@ -1,18 +1,4 @@
 import { defineConfig } from "vitepress";
-import { dirname, relative, resolve, sep } from "node:path";
-import { fileURLToPath } from "node:url";
-import {
-  documentationRewrites,
-  documentationSections,
-} from "./documentation.js";
-
-const documentationRoot = fileURLToPath(new URL("..", import.meta.url));
-const rewrites: Record<string, string> = {
-  ...documentationRewrites,
-  "README.md": "documentation.md",
-  "specs/README.md": "specs/index.md",
-  "adr/README.md": "adr/index.md",
-};

 export default defineConfig({
  title: "REA",
@@ -20,92 +6,110 @@ export default defineConfig({
    "Reverse engineer binaries, applications, and runtime behavior with one CLI and MCP server.",
  lang: "en-US",
  base: "/rea/",
-  rewrites,
-  markdown: {
-    config(md) {
-      // Repository links resolve from their physical source. Render them from
-      // the stable public route instead, including links across categories.
-      md.core.ruler.after("inline", "documentation-source-links", (state) => {
-        const physicalPath =
-          state.env.realPath ??
-          (state.env.relativePath
-            ? resolve(documentationRoot, state.env.relativePath)
-            : null);
-        if (physicalPath === null) return;
-        const renderedPath =
-          state.env.path ??
-          resolve(
-            documentationRoot,
-            rewrites[state.env.relativePath] ?? state.env.relativePath,
-          );
-        for (const block of state.tokens) {
-          for (const token of block.children ?? []) {
-            const attribute =
-              token.type === "link_open"
-                ? "href"
-                : token.type === "image"
-                  ? "src"
-                  : null;
-            if (attribute === null) continue;
-            const destination = token.attrGet(attribute);
-            if (
-              !destination ||
-              /^(?:[a-z][a-z\d+.-]*:|[/#])/iu.test(destination)
-            )
-              continue;
-            const separator = destination.search(/[?#]/u);
-            const path =
-              separator === -1 ? destination : destination.slice(0, separator);
-            const suffix = separator === -1 ? "" : destination.slice(separator);
-            const source = relative(
-              documentationRoot,
-              resolve(dirname(physicalPath), path),
-            )
-              .split(sep)
-              .join("/");
-            const rendered = relative(
-              dirname(renderedPath),
-              resolve(
-                documentationRoot,
-                source.startsWith("public/")
-                  ? source.slice("public/".length)
-                  : (rewrites[source] ?? source),
-              ),
-            )
-              .split(sep)
-              .join("/");
-            token.attrSet(attribute, rendered + suffix);
-          }
-        }
-      });
-    },
-  },
  srcExclude: ["readme/**"],
  themeConfig: {
    nav: [
      { text: "Get started", link: "/installation" },
-      { text: "Documentation", link: "/documentation" },
      { text: "Reference", link: "/mcp-contracts" },
      { text: "Roadmap", link: "/roadmap" },
    ],
    sidebar: [
      {
-        text: "Documentation directory",
+        text: "Getting started",
        items: [
-          { text: "All guides", link: "/documentation" },
-          { text: "Authoring conventions", link: "/development/documentation" },
-          { text: "Feature specifications", link: "/specs/" },
-          { text: "Architecture decisions", link: "/adr/" },
+          { text: "Installation and setup", link: "/installation" },
+          { text: "Client configuration", link: "/client-configuration" },
+          { text: "CLI and Evidence", link: "/cli" },
+          { text: "Agent prompts", link: "/mcp-prompts" },
+          { text: "Roadmap", link: "/roadmap" },
+        ],
+      },
+      {
+        text: "Investigation guides",
+        items: [
+          { text: "Native binaries", link: "/native-investigation" },
+          { text: "Go build metadata", link: "/go-binaries" },
+          { text: "IL2CPP metadata", link: "/il2cpp-metadata" },
+          { text: "Model artifacts", link: "/model-artifacts" },
+          { text: "Rust dependencies", link: "/rust-binaries" },
+          { text: "PE certificates", link: "/pe-certificates" },
+          { text: "PE imports", link: "/pe-imports" },
+          { text: "PE TLS/load config", link: "/pe-load-config" },
+          { text: "ELF notes", link: "/elf-notes" },
+          { text: "Apple IPS crash reports", link: "/apple-ips" },
+          { text: "Linux kernel modules", link: "/kernel-modules" },
+          { text: "CPython pyc files", link: "/python-pyc" },
+          { text: "Erlang BEAM", link: "/erlang-beam" },
+          {
+            text: "JavaScript and Electron",
+            link: "/javascript-artifact-reconstruction",
+          },
+          {
+            text: "JavaScript workflows",
+            link: "/javascript-application-workflows",
+          },
+          { text: "Browser observation", link: "/browser-observation" },
+          {
+            text: "Web network captures",
+            link: "/web-network-captures",
+          },
+          {
+            text: "Build RL environments",
+            link: "/agent-environments-quickstart",
+          },
+          { text: "Environment reference", link: "/agent-environments" },
+          { text: "Electron observation", link: "/electron-observation" },
+          { text: "Electron fuses", link: "/electron-fuses" },
+          { text: "Process capture", link: "/process-capture" },
+          { text: ".NET assemblies", link: "/managed-code-analysis" },
+          {
+            text: "Python packaged applications",
+            link: "/python-packaged-applications",
+          },
+          { text: "Android applications", link: "/android-analysis" },
+          { text: "Apple applications", link: "/apple-application-analysis" },
+          { text: "Desktop installations", link: "/desktop-applications" },
+          { text: "Firmware", link: "/firmware-analysis" },
+          { text: "iNES containers", link: "/ines-containers" },
+          { text: "SQLite databases", link: "/sqlite-databases" },
+          { text: "Packet captures", link: "/packet-captures" },
+          { text: "Signal recordings", link: "/signal-recordings" },
+        ],
+      },
+      {
+        text: "Provider guides",
+        collapsed: true,
+        items: [
+          { text: "IDA", link: "/ida-provider" },
+          { text: "Kuna", link: "/kuna-provider" },
+          { text: "Ghidra on Windows", link: "/windows-ghidra-p0" },
+          { text: "Ghidra DOS analysis", link: "/ghidra-dos" },
+          { text: "Ghidra raw binary", link: "/raw-binary" },
+          { text: "Ghidra NativeAOT", link: "/ghidra-nativeaot" },
+          { text: "Ghidra PowerPC", link: "/ghidra-ppc" },
+          { text: "Ghidra GameCube DOL", link: "/ghidra-dol" },
+          { text: "Ghidra semantics", link: "/ghidra-provider" },
+        ],
+      },
+      {
+        text: "Reference and development",
+        collapsed: true,
+        items: [
+          { text: "MCP contracts", link: "/mcp-contracts" },
+          { text: "Tool design", link: "/tool-design" },
+          {
+            text: "Admission limits and recovery",
+            link: "/design/limits-and-recovery",
+          },
+          { text: "Testing", link: "/testing" },
+          { text: "Client verification", link: "/client-verification" },
+          {
+            text: "Reconstruction readiness",
+            link: "/reconstruction-readiness",
+          },
+          { text: "Releasing", link: "/releasing" },
        ],
      },
-      ...documentationSections.map((section) => ({
-        text: section.text,
-        collapsed: section.text !== "Getting started",
-        items: section.items.map((item) => ({
-          text: item.text,
-          link: item.route,
-        })),
-      })),
    ],
    search: { provider: "local" },
    socialLinks: [
@@ -1,654 +0,0 @@
-// Authored guide ownership: physical sources and stable public routes.
-export const documentationSections = [
-  {
-    text: "Getting started",
-    items: [
-      {
-        text: "Installation and setup",
-        source: "getting-started/installation.md",
-        route: "/installation",
-      },
-      {
-        text: "Client configuration and troubleshooting",
-        source: "getting-started/client-configuration.md",
-        route: "/client-configuration",
-      },
-      {
-        text: "CLI and Evidence",
-        source: "getting-started/cli.md",
-        route: "/cli",
-      },
-      {
-        text: "Guided MCP prompts and completion",
-        source: "getting-started/mcp-prompts.md",
-        route: "/mcp-prompts",
-      },
-    ],
-  },
-  {
-    text: "Native binaries",
-    items: [
-      {
-        text: "Native binary investigation",
-        source: "guides/native/native-investigation.md",
-        route: "/native-investigation",
-      },
-      {
-        text: "Go binary build metadata",
-        source: "guides/native/go-binaries.md",
-        route: "/go-binaries",
-      },
-      {
-        text: "Offline binary diagnostics",
-        source: "guides/native/binary-diagnostics.md",
-        route: "/binary-diagnostics",
-      },
-      {
-        text: "Recorded crash evidence",
-        source: "guides/native/recorded-crashes.md",
-        route: "/recorded-crashes",
-      },
-    ],
-  },
-  {
-    text: "JavaScript and Electron",
-    items: [
-      {
-        text: "JavaScript Application Graph",
-        source: "guides/javascript/javascript-application-graph.md",
-        route: "/javascript-application-graph",
-      },
-      {
-        text: "Cross-layer JavaScript application workflows",
-        source: "guides/javascript/javascript-application-workflows.md",
-        route: "/javascript-application-workflows",
-      },
-      {
-        text: "JavaScript artifact reconstruction",
-        source: "guides/javascript/javascript-artifact-reconstruction.md",
-        route: "/javascript-artifact-reconstruction",
-      },
-      {
-        text: "JavaScript source recovery",
-        source: "guides/javascript/javascript-recovery.md",
-        route: "/javascript-recovery",
-      },
-      {
-        text: "Passive Node and Electron runtime observation",
-        source: "guides/javascript/javascript-runtime-observation.md",
-        route: "/javascript-runtime-observation",
-      },
-      {
-        text: "JavaScript static/runtime reconciliation",
-        source: "guides/javascript/javascript-runtime-reconciliation.md",
-        route: "/javascript-runtime-reconciliation",
-      },
-      {
-        text: "Electron file-page observation",
-        source: "guides/javascript/electron-observation.md",
-        route: "/electron-observation",
-      },
-    ],
-  },
-  {
-    text: "Browser and captured websites",
-    items: [
-      {
-        text: "Website observation with CDP",
-        source: "guides/web/browser-observation.md",
-        route: "/browser-observation",
-      },
-      {
-        text: "Browser scenario contract",
-        source: "guides/web/browser-scenario-contract.md",
-        route: "/browser-scenario-contract",
-      },
-      {
-        text: "Website runtime source attribution",
-        source: "guides/web/web-runtime.md",
-        route: "/web-runtime",
-      },
-      {
-        text: "Historical web network captures",
-        source: "guides/web/web-network-captures.md",
-        route: "/web-network-captures",
-      },
-      {
-        text: "HTTP/3 capture lab",
-        source: "http3-capture-lab.md",
-        route: "/http3-capture-lab",
-      },
-      {
-        text: "Captured website source locations",
-        source: "guides/web/web-source-location.md",
-        route: "/web-source-location",
-      },
-      {
-        text: "Captured website module relationships",
-        source: "guides/web/website-module-trace.md",
-        route: "/website-module-trace",
-      },
-      {
-        text: "Captured website scripts and static JavaScript analysis",
-        source: "guides/web/website-script-export.md",
-        route: "/website-script-export",
-      },
-    ],
-  },
-  {
-    text: "Android applications",
-    items: [
-      {
-        text: "Static Android APK analysis",
-        source: "guides/android/android-analysis.md",
-        route: "/android-analysis",
-      },
-      {
-        text: "Apktool resource decoding",
-        source: "guides/android/apktool-resource-analysis.md",
-        route: "/apktool-resource-analysis",
-      },
-      {
-        text: "ADB device inspection and acquisition",
-        source: "guides/android/adb-device-analysis.md",
-        route: "/adb-device-analysis",
-      },
-      {
-        text: "Flutter build identification",
-        source: "guides/android/flutter-analysis.md",
-        route: "/flutter-analysis",
-      },
-    ],
-  },
-  {
-    text: "Apple applications",
-    items: [
-      {
-        text: "Apple Application Inventory Projection",
-        source: "guides/apple/apple-application-analysis.md",
-        route: "/apple-application-analysis",
-      },
-    ],
-  },
-  {
-    text: ".NET assemblies",
-    items: [
-      {
-        text: "Managed-code analysis",
-        source: "guides/managed/managed-code-analysis.md",
-        route: "/managed-code-analysis",
-      },
-    ],
-  },
-  {
-    text: "Firmware",
-    items: [
-      {
-        text: "Firmware analysis",
-        source: "guides/firmware/firmware-analysis.md",
-        route: "/firmware-analysis",
-      },
-    ],
-  },
-  {
-    text: "HarmonyOS packages",
-    items: [
-      {
-        text: "Static HarmonyOS package inventory",
-        source: "guides/harmony/harmony-analysis.md",
-        route: "/harmony-analysis",
-      },
-    ],
-  },
-  {
-    text: "WebAssembly",
-    items: [
-      {
-        text: "Offline WebAssembly artifacts",
-        source: "guides/wasm/wasm-artifacts.md",
-        route: "/wasm-artifacts",
-      },
-    ],
-  },
-  {
-    text: "EVM contracts",
-    items: [
-      {
-        text: "Offline EVM bytecode",
-        source: "guides/evm/evm-bytecode.md",
-        route: "/evm-bytecode",
-      },
-    ],
-  },
-  {
-    text: "Databases and recorded packets",
-    items: [
-      {
-        text: "SQLite database snapshots",
-        source: "guides/data/sqlite-databases.md",
-        route: "/sqlite-databases",
-      },
-      {
-        text: "Recorded packet capture inspection",
-        source: "guides/data/packet-captures.md",
-        route: "/packet-captures",
-      },
-      {
-        text: "Packet capture summaries",
-        source: "guides/data/pcap-analysis.md",
-        route: "/pcap-analysis",
-      },
-    ],
-  },
-  {
-    text: "Process capture and instrumentation",
-    items: [
-      {
-        text: "Process capture",
-        source: "guides/runtime/process-capture.md",
-        route: "/process-capture",
-      },
-      {
-        text: "Frida instrumentation",
-        source: "guides/runtime/frida-instrumentation.md",
-        route: "/frida-instrumentation",
-      },
-    ],
-  },
-  {
-    text: "Provider setup and formats",
-    items: [
-      {
-        text: "Ghidra provider semantics",
-        source: "providers/ghidra-provider.md",
-        route: "/ghidra-provider",
-      },
-      {
-        text: "DOS MZ and COM analysis with Ghidra",
-        source: "providers/ghidra-dos.md",
-        route: "/ghidra-dos",
-      },
-      {
-        text: "Optional NativeAOT metadata recovery",
-        source: "providers/ghidra-nativeaot.md",
-        route: "/ghidra-nativeaot",
-      },
-      {
-        text: "MIPS ELF analysis through Ghidra",
-        source: "providers/ghidra-mips.md",
-        route: "/ghidra-mips",
-      },
-      {
-        text: "PSP static ELF analysis through Ghidra",
-        source: "providers/ghidra-psp.md",
-        route: "/ghidra-psp",
-      },
-      {
-        text: "RISC-V ELF analysis through Ghidra",
-        source: "providers/ghidra-riscv.md",
-        route: "/ghidra-riscv",
-      },
-      {
-        text: "Windows Ghidra P0",
-        source: "providers/windows-ghidra-p0.md",
-        route: "/windows-ghidra-p0",
-      },
-      {
-        text: "Headerless raw-binary analysis with Ghidra",
-        source: "providers/raw-binary.md",
-        route: "/raw-binary",
-      },
-      {
-        text: "IDA provider",
-        source: "providers/ida-provider.md",
-        route: "/ida-provider",
-      },
-      {
-        text: "JEB instrumentation and analysis",
-        source: "providers/jeb-analysis.md",
-        route: "/jeb-analysis",
-      },
-    ],
-  },
-  {
-    text: "Contracts and evidence",
-    items: [
-      {
-        text: "MCP runtime contracts",
-        source: "reference/mcp-contracts.md",
-        route: "/mcp-contracts",
-      },
-      {
-        text: "Reconstruction obligation ledgers",
-        source: "reference/reconstruction-obligation-ledgers.md",
-        route: "/reconstruction-obligation-ledgers",
-      },
-    ],
-  },
-  {
-    text: "Development and verification",
-    items: [
-      {
-        text: "Settings and recovery",
-        source: "design/limits-and-recovery.md",
-        route: "/design/limits-and-recovery",
-      },
-      {
-        text: "MCP tool design",
-        source: "development/tool-design.md",
-        route: "/tool-design",
-      },
-      {
-        text: "Testing REA",
-        source: "development/testing.md",
-        route: "/testing",
-      },
-      {
-        text: "Client and agent verification",
-        source: "development/client-verification.md",
-        route: "/client-verification",
-      },
-      {
-        text: "Reconstruction readiness conformance",
-        source: "development/reconstruction-readiness.md",
-        route: "/reconstruction-readiness",
-      },
-      {
-        text: "Releasing REA",
-        source: "development/releasing.md",
-        route: "/releasing",
-      },
-      {
-        text: "REA roadmap",
-        source: "development/roadmap.md",
-        route: "/roadmap",
-      },
-    ],
-  },
-  {
-    text: "Release migrations",
-    items: [
-      {
-        text: "Upgrading from REA 6.1 to 6.2",
-        source: "migrations/migration-6.2.md",
-        route: "/migration-6.2",
-      },
-    ],
-  },
-  {
-    text: "Signal recordings",
-    items: [
-      {
-        text: "Recorded signal inspection",
-        source: "guides/signals/signal-recordings.md",
-        route: "/signal-recordings",
-      },
-    ],
-  },
-  {
-    text: "Additional guides",
-    items: [
-      {
-        text: "Offline API contract inventory",
-        source: "api-contracts.md",
-        route: "/api-contracts",
-      },
-      {
-        text: "Bun standalone executables",
-        source: "bun-standalone.md",
-        route: "/bun-standalone",
-      },
-      {
-        text: "Capability composition and ownership",
-        source: "capability-composition.md",
-        route: "/capability-composition",
-      },
-      {
-        text: ".NET single-file bundles",
-        source: "dotnet-bundles.md",
-        route: "/dotnet-bundles",
-      },
-      {
-        text: "ESP flash images",
-        source: "esp-flash-image.md",
-        route: "/esp-flash-image",
-      },
-      {
-        text: "U-Boot FIT images",
-        source: "fit-images.md",
-        route: "/fit-images",
-      },
-      {
-        text: "Measure MCP catalog costs in Codex",
-        source: "mcp-catalog-evaluation.md",
-        route: "/mcp-catalog-evaluation",
-      },
-      {
-        text: "Offline Playwright traces",
-        source: "playwright-traces.md",
-        route: "/playwright-traces",
-      },
-      {
-        text: "Testing lanes and provider verification",
-        source: "testing-lanes.md",
-        route: "/testing-lanes",
-      },
-      {
-        text: "UF2 and DfuSe images",
-        source: "uf2-dfuse.md",
-        route: "/uf2-dfuse",
-      },
-      {
-        text: "WeChat mini-program wxapkg archives",
-        source: "wxapkg.md",
-        route: "/wxapkg",
-      },
-      {
-        text: "Binary hardening",
-        source: "binary-hardening.md",
-        route: "/binary-hardening",
-      },
-      {
-        text: "Desktop application capture",
-        source: "desktop-application-capture.md",
-        route: "/desktop-application-capture",
-      },
-      {
-        text: "Desktop application export",
-        source: "desktop-application-export.md",
-        route: "/desktop-application-export",
-      },
-      {
-        text: "Desktop application state",
-        source: "desktop-application-state.md",
-        route: "/desktop-application-state",
-      },
-      {
-        text: "Desktop application tasks",
-        source: "desktop-application-tasks.md",
-        route: "/desktop-application-tasks",
-      },
-      {
-        text: "Desktop build computer",
-        source: "desktop-build-computer.md",
-        route: "/desktop-build-computer",
-      },
-      {
-        text: "Desktop build witness",
-        source: "desktop-build-witness.md",
-        route: "/desktop-build-witness",
-      },
-      {
-        text: "iNES containers",
-        source: "ines-containers.md",
-        route: "/ines-containers",
-      },
-      {
-        text: "Build RL environments with REA",
-        source: "agent-environments-quickstart.md",
-        route: "/agent-environments-quickstart",
-      },
-      {
-        text: "Agent environments from recorded captures",
-        source: "agent-environments.md",
-        route: "/agent-environments",
-      },
-      {
-        text: "APK signature schemes",
-        source: "apk-signature.md",
-        route: "/apk-signature",
-      },
-      {
-        text: "Apple IPS crash reports",
-        source: "apple-ips.md",
-        route: "/apple-ips",
-      },
-      {
-        text: "Static analysis in GitHub Actions",
-        source: "ci-analysis.md",
-        route: "/ci-analysis",
-      },
-      {
-        text: "Desktop installation directories",
-        source: "desktop-applications.md",
-        route: "/desktop-applications",
-      },
-      {
-        text: "Flattened devicetree inspection",
-        source: "devicetree.md",
-        route: "/devicetree",
-      },
-      {
-        text: "Electron fuse state",
-        source: "electron-fuses.md",
-        route: "/electron-fuses",
-      },
-      { text: "ELF note tables", source: "elf-notes.md", route: "/elf-notes" },
-      {
-        text: "Erlang BEAM files",
-        source: "erlang-beam.md",
-        route: "/erlang-beam",
-      },
-      { text: "ESP images", source: "esp-image.md", route: "/esp-image" },
-      {
-        text: "GameCube DOL analysis through Ghidra",
-        source: "ghidra-dol.md",
-        route: "/ghidra-dol",
-      },
-      {
-        text: "PowerPC ELF analysis through Ghidra",
-        source: "ghidra-ppc.md",
-        route: "/ghidra-ppc",
-      },
-      {
-        text: "Godot PCK archives",
-        source: "godot-pck.md",
-        route: "/godot-pck",
-      },
-      {
-        text: "Static CUDA and HIP code objects",
-        source: "gpu-code-objects.md",
-        route: "/gpu-code-objects",
-      },
-      {
-        text: "Intel HEX and S-record images",
-        source: "hex-records.md",
-        route: "/hex-records",
-      },
-      {
-        text: "IL2CPP metadata",
-        source: "il2cpp-metadata.md",
-        route: "/il2cpp-metadata",
-      },
-      {
-        text: "Static JavaScript route inventory",
-        source: "javascript-route-inventory.md",
-        route: "/javascript-route-inventory",
-      },
-      {
-        text: "Linux kernel modules",
-        source: "kernel-modules.md",
-        route: "/kernel-modules",
-      },
-      {
-        text: "Kuna provider",
-        source: "kuna-provider.md",
-        route: "/kuna-provider",
-      },
-      {
-        text: "Model file declarations",
-        source: "model-artifacts.md",
-        route: "/model-artifacts",
-      },
-      {
-        text: "Match native functions across builds",
-        source: "native-function-matching.md",
-        route: "/native-function-matching",
-      },
-      {
-        text: "Node.js single executable applications",
-        source: "node-sea.md",
-        route: "/node-sea",
-      },
-      {
-        text: "PE Authenticode certificate tables",
-        source: "pe-certificates.md",
-        route: "/pe-certificates",
-      },
-      {
-        text: "PE import and delay-load tables",
-        source: "pe-imports.md",
-        route: "/pe-imports",
-      },
-      {
-        text: "PE TLS callbacks and load configuration",
-        source: "pe-load-config.md",
-        route: "/pe-load-config",
-      },
-      {
-        text: "Python packaged applications",
-        source: "python-packaged-applications.md",
-        route: "/python-packaged-applications",
-      },
-      {
-        text: "CPython pyc inspection",
-        source: "python-pyc.md",
-        route: "/python-pyc",
-      },
-      {
-        text: "Reconstruction coverage",
-        source: "reconstruction-coverage.md",
-        route: "/reconstruction-coverage",
-      },
-      {
-        text: "Reverse-engineering tool integrations",
-        source: "reverse-engineering-tools.md",
-        route: "/reverse-engineering-tools",
-      },
-      {
-        text: "Rust binary dependency metadata",
-        source: "rust-binaries.md",
-        route: "/rust-binaries",
-      },
-      {
-        text: "U-Boot legacy uImage containers",
-        source: "uimage.md",
-        route: "/uimage",
-      },
-      {
-        text: "UnityFS AssetBundle archives",
-        source: "unityfs.md",
-        route: "/unityfs",
-      },
-    ],
-  },
-];
-
-export const documentationRewrites = Object.fromEntries(
-  documentationSections.flatMap((section) =>
-    section.items.flatMap((item) => {
-      const target = `${item.route.slice(1)}.md`;
-      return item.source === target ? [] : [[item.source, target]];
-    }),
-  ),
-);
@@ -1,195 +0,0 @@
-# Documentation directory
-
-REA documentation is organized by reader task and document owner. This directory
-links every authored guide; the [site](https://rea.tools/) also serves separate
-product pages. The VitePress documentation source is this `docs/` tree.
-
-## Getting started
-
- [Installation and setup](getting-started/installation.md)
- [Client configuration and troubleshooting](getting-started/client-configuration.md)
- [CLI and Evidence](getting-started/cli.md)
- [Guided MCP prompts and completion](getting-started/mcp-prompts.md)
-
-## Native binaries
-
- [Native binary investigation](guides/native/native-investigation.md)
- [Go binary build metadata](guides/native/go-binaries.md)
- [Offline binary diagnostics](guides/native/binary-diagnostics.md)
- [Recorded crash evidence](guides/native/recorded-crashes.md)
-
-## JavaScript and Electron
-
- [JavaScript Application Graph](guides/javascript/javascript-application-graph.md)
- [Cross-layer JavaScript application workflows](guides/javascript/javascript-application-workflows.md)
- [JavaScript artifact reconstruction](guides/javascript/javascript-artifact-reconstruction.md)
- [JavaScript source recovery](guides/javascript/javascript-recovery.md)
- [Passive Node and Electron runtime observation](guides/javascript/javascript-runtime-observation.md)
- [JavaScript static/runtime reconciliation](guides/javascript/javascript-runtime-reconciliation.md)
- [Electron file-page observation](guides/javascript/electron-observation.md)
-
-## Browser and captured websites
-
- [Website observation with CDP](guides/web/browser-observation.md)
- [Browser scenario contract](guides/web/browser-scenario-contract.md)
- [Website runtime source attribution](guides/web/web-runtime.md)
- [Historical web network captures](guides/web/web-network-captures.md)
- [HTTP/3 capture lab](http3-capture-lab.md)
- [Captured website source locations](guides/web/web-source-location.md)
- [Captured website module relationships](guides/web/website-module-trace.md)
- [Captured website scripts and static JavaScript analysis](guides/web/website-script-export.md)
-
-## Android applications
-
- [Static Android APK analysis](guides/android/android-analysis.md)
- [Apktool resource decoding](guides/android/apktool-resource-analysis.md)
- [ADB device inspection and acquisition](guides/android/adb-device-analysis.md)
- [Flutter build identification](guides/android/flutter-analysis.md)
-
-## Apple applications
-
- [Apple Application Inventory Projection](guides/apple/apple-application-analysis.md)
-
-## .NET assemblies
-
- [Managed-code analysis](guides/managed/managed-code-analysis.md)
-
-## Firmware
-
- [Firmware analysis](guides/firmware/firmware-analysis.md)
-
-## HarmonyOS packages
-
- [Static HarmonyOS package inventory](guides/harmony/harmony-analysis.md)
-
-## WebAssembly
-
- [Offline WebAssembly artifacts](guides/wasm/wasm-artifacts.md)
-
-## EVM contracts
-
- [Offline EVM bytecode](guides/evm/evm-bytecode.md)
-
-## Databases and recorded packets
-
- [SQLite database snapshots](guides/data/sqlite-databases.md)
- [Recorded packet capture inspection](guides/data/packet-captures.md)
- [Packet capture summaries](guides/data/pcap-analysis.md)
-
-## Process capture and instrumentation
-
- [Process capture](guides/runtime/process-capture.md)
- [Frida instrumentation](guides/runtime/frida-instrumentation.md)
-
-## Signal recordings
-
- [Recorded signal inspection](guides/signals/signal-recordings.md)
-
-## Provider setup and formats
-
- [Ghidra provider semantics](providers/ghidra-provider.md)
- [DOS MZ and COM analysis with Ghidra](providers/ghidra-dos.md)
- [Optional NativeAOT metadata recovery](providers/ghidra-nativeaot.md)
- [MIPS ELF analysis through Ghidra](providers/ghidra-mips.md)
- [PSP static ELF analysis through Ghidra](providers/ghidra-psp.md)
- [RISC-V ELF analysis through Ghidra](providers/ghidra-riscv.md)
- [Windows Ghidra P0](providers/windows-ghidra-p0.md)
- [Headerless raw-binary analysis with Ghidra](providers/raw-binary.md)
- [IDA provider](providers/ida-provider.md)
- [JEB instrumentation and analysis](providers/jeb-analysis.md)
-
-## Contracts and evidence
-
- [MCP runtime contracts](reference/mcp-contracts.md)
- [Reconstruction obligation ledgers](reference/reconstruction-obligation-ledgers.md)
-
-## Development and verification
-
- [Settings and recovery](design/limits-and-recovery.md)
- [MCP tool design](development/tool-design.md)
- [Testing REA](development/testing.md)
- [Client and agent verification](development/client-verification.md)
- [Reconstruction readiness conformance](development/reconstruction-readiness.md)
- [Releasing REA](development/releasing.md)
- [REA roadmap](development/roadmap.md)
-
-## Release migrations
-
- [Upgrading from REA 6.1 to 6.2](migrations/migration-6.2.md)
-
-## Architecture and authoring
-
- [Architecture map](https://github.com/morluto/rea/blob/main/docs/architecture/architecture.mermaid)
- [Documentation ownership and contribution model](development/documentation.md)
- [Feature specifications](specs/README.md)
- [Architectural decision records](adr/README.md)
-
-## Machine-owned documentation
-
-| Path                                      | Owner and update command                                                                  |
-| ----------------------------------------- | ----------------------------------------------------------------------------------------- |
-| `public/product-catalog.json`             | Ignored contract projection; `npm run docs:generate`                                      |
-| `verification/managed-conformance-*.json` | Ignored managed conformance projections; `npm run evidence:generate`                      |
-| `error-contract.schema.json`              | Tracked schema from contracts; `npm run docs:error-schema`                                |
-| `user-visible-errors.csv`                 | Authored error classification inventory; preserve its schema                              |
-| `releases/<version>.contributions.json`   | Durable release contribution record; follow the [release guide](development/releasing.md) |
-| `assets/`                                 | Shared authored images referenced by guides                                               |
-
-Do not edit generated catalogs or evidence to change product facts. Change their
-canonical contracts or producer and regenerate. Historical release records retain
-the exact commit messages and references from the release they describe.
-
-## Additional guides
-
- [Offline API contract inventory](api-contracts.md)
- [Bun standalone executables](bun-standalone.md)
- [Capability composition and ownership](capability-composition.md)
- [.NET single-file bundles](dotnet-bundles.md)
- [ESP flash images](esp-flash-image.md)
- [U-Boot FIT images](fit-images.md)
- [Measure MCP catalog costs in Codex](mcp-catalog-evaluation.md)
- [Offline Playwright traces](playwright-traces.md)
- [Testing lanes and provider verification](testing-lanes.md)
- [UF2 and DfuSe images](uf2-dfuse.md)
- [WeChat mini-program wxapkg archives](wxapkg.md)
- [Binary hardening](binary-hardening.md)
- [Desktop application capture](desktop-application-capture.md)
- [Desktop application export](desktop-application-export.md)
- [Desktop application state](desktop-application-state.md)
- [Desktop application tasks](desktop-application-tasks.md)
- [Desktop build computer](desktop-build-computer.md)
- [Desktop build witness](desktop-build-witness.md)
- [iNES containers](ines-containers.md)
- [Build RL environments with REA](agent-environments-quickstart.md)
- [Agent environments from recorded captures](agent-environments.md)
- [APK signature schemes](apk-signature.md)
- [Apple IPS crash reports](apple-ips.md)
- [Static analysis in GitHub Actions](ci-analysis.md)
- [Desktop installation directories](desktop-applications.md)
- [Flattened devicetree inspection](devicetree.md)
- [Electron fuse state](electron-fuses.md)
- [ELF note tables](elf-notes.md)
- [Erlang BEAM files](erlang-beam.md)
- [ESP images](esp-image.md)
- [GameCube DOL analysis through Ghidra](ghidra-dol.md)
- [PowerPC ELF analysis through Ghidra](ghidra-ppc.md)
- [Godot PCK archives](godot-pck.md)
- [Static CUDA and HIP code objects](gpu-code-objects.md)
- [Intel HEX and S-record images](hex-records.md)
- [IL2CPP metadata](il2cpp-metadata.md)
- [Static JavaScript route inventory](javascript-route-inventory.md)
- [Linux kernel modules](kernel-modules.md)
- [Kuna provider](kuna-provider.md)
- [Model file declarations](model-artifacts.md)
- [Match native functions across builds](native-function-matching.md)
- [Node.js single executable applications](node-sea.md)
- [PE Authenticode certificate tables](pe-certificates.md)
- [PE import and delay-load tables](pe-imports.md)
- [PE TLS callbacks and load configuration](pe-load-config.md)
- [Python packaged applications](python-packaged-applications.md)
- [CPython pyc inspection](python-pyc.md)
- [Reconstruction coverage](reconstruction-coverage.md)
- [Reverse-engineering tool integrations](reverse-engineering-tools.md)
- [Rust binary dependency metadata](rust-binaries.md)
- [U-Boot legacy uImage containers](uimage.md)
- [UnityFS AssetBundle archives](unityfs.md)
@@ -25,21 +25,7 @@ REA never installs the Android SDK, an emulator, or a system image.
 Readiness is `rea inspect-adb-client`: it runs `adb version` and reports the
 resolved binary, its version, and where it was selected from. A missing
 binary reports `capability_unavailable` with the `REA_ADB_PATH` remediation
-rather than attempting an installation. A path that cannot resolve to a file
-(`ENOENT`, `ENOTDIR`, `ELOOP` or `ENAMETOOLONG`) is reported as missing. A
-selected path the host refuses to execute, such as a directory or a file
-without execute permission (`EACCES`) or one the host does not permit
-(`EPERM`), and any other spawn error report `capability_unavailable` naming
-that path. Exhausted host capacity (`EAGAIN`, `EMFILE`, `ENFILE` or `ENOMEM`)
-is not a configuration failure. `inspect_adb_client`, and any device
-operation whose adb cannot start at its version probe or at a later adb
-command, report a retryable `capacity` resource constraint rather than a
-capability refusal or an adb protocol failure; the `binary_session` inventory
-reports the provider as `runtime_unavailable`. Both say the host could not
-start adb and ask for a retry after freeing processes or descriptors, without
-blaming `REA_ADB_PATH`. When adb never started, the refusal diagnostics record
-the spawn error as `filesystem_error` with `path_source`, never as an
-`exit_code`.
+rather than attempting an installation.
 The `binary_session` inventory uses the same bounded client-version probe; it
 does not query devices, start the adb server, or establish that a requested
 serial is reachable. Device state is checked by each device operation.
@@ -217,18 +203,12 @@ and during shutdown.
  `uninstall_adb_package` declare `mutatesTarget` and never run implicitly:
  pushes check for existing device files before transfer and refuse them
  unless `overwrite` is set. A failed or unexpected existence probe stops
-  transfer even with `overwrite`. A completed `test -e` exit of 1 establishes
-  absence only with empty stdout and either empty stderr or a recognized,
-  completed adb-server startup notice sequence. Startup notices are host
-  observations, not remote-path diagnostics; successful push receipts retain
-  them in `raw_result.device_path_probes`. Incomplete startup, extra diagnostics,
-  truncation and cancellation do not establish absence. The check is not atomic, so a different
+  transfer even with `overwrite`; only a clean `test -e` exit of 1 with no
+  output is interpreted as absence. The check is not atomic, so a different
  process can create the path before `adb push` writes it. When available, the device's
-  `sha256sum` verifies the transfer. A missing command, output without a
-  recognizable digest, or host capacity that prevents the digest check from
-  starting reports `device_digest_source: "unavailable"` with an
-  unverified-transfer limitation rather than a retryable error; installs
-  preserve the
+  `sha256sum` verifies the transfer. A missing command or output without a
+  recognizable digest reports `device_digest_source: "unavailable"` with an
+  unverified-transfer limitation; installs preserve the
  device's `Failure [...]` reason verbatim.
 - **Producer identity stays attached.** Every result embeds the producing
  adb client (`binary_path`, `path_source`, `version`, `installed_path`).
@@ -288,7 +268,7 @@ Record: verified against adb 34.0.5 on Linux against an Android 14
 (API 34) x86_64 emulator — all operations above, a 224-package inventory,
 287 services, 92 features, a real two-APK split set pulled with byte-exact
 digests, a verified push/pull roundtrip, a 1.3 MB screen capture, and the
-complete package lifecycle; see `docs/development/testing.md` for the lane summary.
+complete package lifecycle; see `docs/testing.md` for the lane summary.

 Intent integer extras use signed decimal text. The ADB argument encoder removes
 redundant leading zeros for Android's radix-sensitive `--ei` parser while retained
@@ -1,9 +0,0 @@
-# Architectural decision records
-
-Store one actual decision per `docs/adr/<domain>/<decision-slug>.md`, without a
-global sequence number. Use meaningful names and the Michael Nygard sections:
-Status, Context, Decision and Consequences. Link each decision from its owning
-feature specification.
-
-See [the authoring guide](../development/documentation.md#feature-lifecycle) for
-the distinction between specifications, roadmaps and isolated decisions.
@@ -11,15 +11,15 @@ with your RL framework to set task goals, check rewards, and run training.

 ## Before you start

-Install [REA and its agent integration](getting-started/installation.md). To record an app,
+Install [REA and its agent integration](installation.md). To record an app,
 you also need a running test instance and a Chrome-family browser. Choose an
 instance where the agent is allowed to create, edit, and delete data. REA
 records the app you provide; you start it and prepare its test data.

 To run the exported environment, install the
 [AgentEnv framework](https://github.com/scaleapi/agentenv-framework#install)
-and start Docker. REA's [compatibility check](development/testing.md#exported-environment-bundles)
-uses AgentEnv version `0.9.1431` with Python 3.12.
+and start Docker. REA's [compatibility check](testing.md#exported-environment-bundles)
+uses AgentEnv version `0.9.1334` with Python 3.12.

 There are two ways to build an environment: ask your agent to record the app,
 or start from a recording you already have.
@@ -52,7 +52,7 @@ work and which need more evidence. The app is used during recording; the
 exported environment runs from the saved data.

 After your agent exports the folder, skip to
-[run the environment](#run-the-environment). The next section is an
+[run the environment](#3-run-the-environment). The next section is an
 alternative for an existing recording.

 ## 2. Or build from a saved recording
@@ -91,8 +91,6 @@ A successful build means the folder was created. Check the report to confirm
 it supports the operations your tasks need. `coverage: null` means the build
 could not prepare state for this environment and it will use replay.

-<a id="run-the-environment"></a>
-
 ## 3. Run the environment

 Whether your agent exported the folder or you built it from a HAR, run it
@@ -30,7 +30,7 @@ rea environment-serve manifest.json --evidence capture.json --port 8765
 ```

 The first command inspects the capture; the second projects the
-[environment manifest](guides/web/web-network-captures.md#environment-manifest) view from
+[environment manifest](web-network-captures.md#environment-manifest) view from
 it, where `view.json` wraps the capture Evidence as the inline source:

 ```json
@@ -163,7 +163,7 @@ at info level; the report is the only output on stdout:

 `coverage` is the state's read views and write plans summarized, and `null`
 when the state is unavailable and the bundle serves replay. The
-[environment coverage](guides/web/web-network-captures.md#environment-coverage) view
+[environment coverage](web-network-captures.md#environment-coverage) view
 reports the same summary for any capture without building, so an agent can
 check it after each recording. The view summarizes the state as derived; it
 does not apply the serve-time admission checks, so for an environment whose
@@ -235,7 +235,7 @@ name `export_environment_bundle`; the others name their stage as
 ## From a browser scenario

 The capture can also come from REA itself: a
-[browser scenario](guides/web/browser-scenario-contract.md) records a scripted session
+[browser scenario](browser-scenario-contract.md) records a scripted session
 in a browser REA launches, and its Evidence is a manifest parent like a HAR
 inspection. Select the `network` event family and response bodies. A replayed
 reply carries up to 256 KiB of a recorded body, but the scenario keeps at most
@@ -321,7 +321,7 @@ declared secret replaced by its redaction marker (a body that redaction had to
 empty replays no body).

 To record writes, sign in through the UI and then send the application's API
-calls with [request steps](guides/web/browser-scenario-contract.md#request-steps): each
+calls with [request steps](browser-scenario-contract.md#request-steps): each
 sends one request to the start origin through the page's own `fetch`, with the
 session's cookies, and a header can carry the CSRF cookie or stored token the
 application's own requests send. A write is served only when the capture shows
@@ -481,7 +481,7 @@ captured text without changing the tool names or schema fields clients use.

 Replay answers each call from one recording, so the answers reflect whichever
 moment of the capture recorded them. The
-[environment state](guides/web/web-network-captures.md#environment-state) view extracts
+[environment state](web-network-captures.md#environment-state) view extracts
 instead the data the capture's reads observed before the first related write:
 entity types with an identity field, entities with their recorded values,
 documents for reads that are not entities, and a render plan per read tool,
@@ -503,14 +503,14 @@ see [Serve from the state](#serve-from-the-state).

 `--host` and `--port` default to `MCP_HOST` and `MCP_PORT` from the
 environment, then to `127.0.0.1` and an ephemeral port, exactly as
-[`rea mcp --http`](getting-started/cli.md#serve-mcp-over-streamable-http) resolves them. The
+[`rea mcp --http`](cli.md#serve-mcp-over-streamable-http) resolves them. The
 bound MCP URL is written to stderr as one JSON log line
 (`"msg":"MCP transport listening"` with `url`); `REA_LOG_LEVEL` overrides that
 log level. `ENVIRONMENT_NAME` renames the served environment; otherwise the
 manifest's `name` is used, and a set but blank value is refused as
 `configuration_invalid` before binding rather than silently falling back. The
 listener serves one MCP client at a time with the same session, `Host` header
-and shutdown contract as [transports](reference/mcp-contracts.md#transports) describes.
+and shutdown contract as [transports](mcp-contracts.md#transports) describes.
 It runs until SIGINT or SIGTERM, then closes the listener, prints one
 `{"status":"stopped", …}` document whose `state` member says whether it served
 from the state, and exits `130` or `143`.
@@ -585,7 +585,7 @@ names the method and path template, then what the tool returns, one level deep:
 `returns a JSON object with fields …`, `returns a JSON array of objects with
 fields …` or `returns a JSON object whose <member> lists objects with fields …`,
 where a list is an array of objects found by the
-[environment state](guides/web/web-network-captures.md#environment-state)'s list rule (the
+[environment state](web-network-captures.md#environment-state)'s list rule (the
 root array, or the one array of objects an envelope carries). Field and member
 names are written as JSON strings, so a captured name cannot read as more of
 the description; a member name too long to show whole is a quoted prefix marked
@@ -641,7 +641,7 @@ rea environment-serve manifest.json --evidence capture.json
 ```

 Before it binds, the server derives the
-[environment state](guides/web/web-network-captures.md#environment-state) the capture
+[environment state](web-network-captures.md#environment-state) the capture
 observed: it runs the `environment-state` view on the capture in-process with
 the manifest's `template_rules` in the same order, exactly as
 `inspect-analysis-view` projects it from the same capture, so the state
@@ -733,7 +733,7 @@ query model may describe supported paging; an empty later page cannot start
 returning earlier entities merely because it was empty in the capture.

 `POST`, `PUT`, `PATCH` and `DELETE` tools are served only when the state's
-[write plan](guides/web/web-network-captures.md#environment-state) for them is served:
+[write plan](web-network-captures.md#environment-state) for them is served:
 the capture's later reads confirmed the effect the plan models. Other write
 tools are not served, so no call claims a change it does not make; each one's
 plan states why in its `reason`. A served write changes the live state, which
@@ -1049,9 +1049,8 @@ unknown recorded status stays unknown; it is not borrowed from another
 record). A bundle with no such tool yields a verifier that checks the count
 only and says so. `tasks/smoke.json` deploys the env on the local
 sandbox and runs that verifier against the env's MCP endpoint; the first run
-also pulls the framework's published infrastructure images from `ghcr.io`,
-building one only if its pull fails, and the run tears everything down when it
-ends.
+also builds the framework's own infrastructure, and the run tears everything
+down when it ends.

 The README written into the bundle records the capture artifact's SHA-256, the
 capture and manifest Evidence ids, the manifest view digest, the served tool
@@ -1187,7 +1186,7 @@ read, not that the write had no other effect.
 ## Compatibility verification

 `npm run verify:agentenv:environment` is the hosted `real-agentenv` lane
-described in [testing](development/testing.md#exported-environment-bundles). It projects
+described in [testing](testing.md#exported-environment-bundles). It projects
 the Grafana-shaped source-owned capture through the built CLI, packs the
 checkout, exports a bundle with `--package-tarball`, runs it with the pinned
 `agentenv-framework` release on the runner's Docker and requires the smoke task
@@ -6,12 +6,12 @@ kept as an unmodified, commit-pinned Git submodule; see
 application workflow and return artifact-bound Evidence inline.

 This family is present on repository main and in npm 4.1.0. Check the
-[released package boundary](../../getting-started/installation.md#released-package-and-main) and the
+[released package boundary](installation.md#released-package-and-main) and the
 connected server's tool list before selecting it.

 On Linux, JADX launches an REA-owned process and requires a procps-compatible
 `ps` on REA's `PATH`; see the shared
-[Linux process prerequisite](../../getting-started/installation.md#linux-owned-process-prerequisite).
+[Linux process prerequisite](installation.md#linux-owned-process-prerequisite).

 ## Optional package delivery

@@ -73,9 +73,6 @@ spellings; the original SDK declaration strings remain unchanged.
 it remains null for unknown provider target SDKs, nonliteral declarations, or
 components with filters targeting API 31 or later that omit the now-required
 explicit declaration. A limitation records the latter validation error.
-As in Android's package parser, an activity, alias or receiver filter without
-an `<action>` is discarded and does not count toward either rule; a service
-keeps such a filter. `intent_filter_count` still counts every declared filter.
 Provider authorities and all inventory dimensions are bounded. `status:
 "partial"` and `limitations` identify omitted declarations or values; a
 capacity limitation appears only when an actual collection limit was reached.
@@ -687,14 +684,14 @@ bounds each upstream call. Timeout recovery reports the effective milliseconds
 and range, with `details.limit` identifying the runtime setting. An invalid
 provider-local launch value can also be repaired by a runtime override; reset
 exposes that invalid launch value again. See the
-[settings design](../../design/limits-and-recovery.md#invalid-launch-configuration).
+[settings design](design/limits-and-recovery.md#invalid-launch-configuration).
 A passing JADX configuration check in `rea doctor` reports its launch-derived
 `operation_timeout_ms`; it does not inspect another running server's overrides. Explicit
 cancellation still ends the operation immediately, and partial observations
 and owned-process cleanup are unchanged. Raising the deadline does not extend
 the bridge's 30-second startup handshake or the upstream **90-second**
 decompilation limit. MCP clients enforce their own tool-call timeouts, and
-setup's derived [client tool timeout](../../getting-started/client-configuration.md) does not include
+setup's derived [client tool timeout](client-configuration.md) does not include
 this setting, so also raise the client timeout when selecting a longer
 deadline.

@@ -1,178 +0,0 @@
-# Offline API contract inventory
-
-`inspect_api_contract` / `rea inspect-api-contract` supports local OpenAPI JSON
-and GraphQL SDL (`format: "graphql-sdl"`). Neither profile contacts endpoints.
-
-## OpenAPI JSON
-
-The default profile reads one local OpenAPI
-3.0, 3.1 or 3.2 JSON document. It inventories inline operation slots under
-`paths`; the facts describe declarations, not implemented, reachable or
-authorized runtime behavior. YAML, AsyncAPI, callbacks/webhooks, schema graphs,
-contract diffs and traffic correlation are outside this version.
-
-The OpenAPI importer never resolves references, opens sibling documents, evaluates
-examples or contacts declared servers. OpenAPI 3.2 `query` and
-`additionalOperations` follow the [Path Item contract](https://spec.openapis.org/oas/v3.2.1.html#path-item-object),
-including case-sensitive additional HTTP method spelling.
-
-## Select a useful answer
-
-MCP defaults to a summary retaining the complete inventory. An optional view
-returns selected facts immediately, taking precedence over `detail`:
-
-```json
-{
-  "path": "/artifacts/openapi.json",
-  "view": {
-    "kind": "api-contract",
-    "collection": "operations",
-    "methods": ["GET"],
-    "limit": 20
-  }
-}
-```
-
-`operations` supports exact `operation_ids`, `operation_keys`, `methods`,
-`paths`, `declared_ids` and `states` filters. Filters combine by intersection;
-empty arrays select nothing. `fields` chooses columns; identity, source pointer,
-state and unknown reason remain. The other collections are
-`path-item-references` (optional `reference_ids`) and `diagnostics` (optional
-`codes`), also with fields and offset/limit. The default page contains 64 rows.
-
-Query a retained result with `inspect_analysis_view`, using the same view and
-`source: {"kind":"retained-evidence","evidence_id":"..."}`. Copy the complete
-parent ID from `normalized_result.parent_evidence_id`, not the summary's own ID.
-These pages use immutable retained facts without rereading the specification.
-Complete Evidence remains available through `get_evidence_bundle`.
-
-CLI defaults to complete Evidence. For a selected answer, save that complete
-Evidence in an absent bundle path:
-
-```sh
-rea inspect-api-contract ./openapi.json --detail summary \
-  --view '{"kind":"api-contract","collection":"operations","methods":["GET"],"limit":20}' \
-  --evidence_output ./contract.evidence.json --json
-```
-
-Later `rea inspect-analysis-view` can read that bundle through an exact
-`evidence-file` source selection, even after the original specification is
-unavailable. Publication never overwrites an existing file. CLI preserves its
-original path spelling in `caller_input_path`; analysis locations and MCP inputs
-use absolute filesystem paths.
-
-## Identity, provenance and coverage
-
-Each operation has an artifact-scoped `operation_id`, an exact method/path
-`operation_key`, an optional `declared_id` from `operationId`, and its original
-JSON Pointer. Keys can correlate exact declarations in a caller-selected pair
-of revisions; they do not establish equivalence across unrelated APIs, renamed
-path templates or runtime handlers. Declared IDs are not assumed unique.
-The artifact includes the verified byte length, SHA-256 and selected path.
-
-Malformed siblings retain useful declarations plus diagnostics. A Path Item
-`$ref`, including a local fragment, remains unresolved; adjacent inline slots
-are unknown because referenced fields may overlap. Missing or malformed paths
-are explicit, and missing required OpenAPI 3.0 paths does not become a complete
-empty inventory. `source_coverage` is limited to inline paths and records that
-reference resolution and full schema validation were not performed. Page
-exhaustion describes the selected rows and never upgrades source coverage.
-
-Structured transport userinfo credentials are excluded from reference URIs;
-`credential_redacted` reports that change, and an ambiguous credential span leaves
-the displayed reference unknown. Ordinary reference query/fragment text and
-names are retained. Original bytes remain in the caller's artifact; complete
-inventory Evidence does not embed the entire source JSON. Duplicate JSON members
-use the shared parser's last-value-wins behavior, recorded in source coverage.
-
-If decoding or later validation fails after a verified read, the typed error
-retains a compact `file-snapshot-hash` observation with the exact path, digest
-and byte length. Syntax diagnostics do not quote source JSON. Cancellation
-does not replace a parser failure that has already completed.
-
-## Resource bounds and verification
-
-The file-byte allowance and conservative expanded-facts allowance are each
-32 MiB resource policies, not OpenAPI format limits. `max_file_bytes` can lower
-the input allowance. Native JSON parsing additionally checks available heap
-against the shared representation-expansion estimate before decoding. The
-shared JSON nesting limit is 1,000, including uninterpreted schema regions.
-Capacity refusals are typed; reply paging does not increase parser allowances.
-
-The committed [Petstore fixture](https://github.com/morluto/rea/blob/b7c8caedd4166e6032c49024cdc6fb1154f1a2df/tests/fixtures/openapi/README.md) is an
-original document from the published application, replayed offline through
-public CLI/MCP tests. These check advertised schemas, complete/selected parity,
-retained paging, partial references, zero requests to a loopback reference
-server and unchanged source bytes. They do not establish runtime endpoint
-behavior or full OpenAPI conformance.
-
-## GraphQL SDL and operation documents
-
-Select `format: "graphql-sdl"` for SDL. Optionally supply `operations_path` to
-one local document containing operations and fragments. Both MCP paths are
-absolute; CLI accepts relative spellings:
-
-```sh
-rea inspect-api-contract ./schema.graphql --contractFormat graphql-sdl \
-  --operationsPath ./queries.graphql --detail summary \
-  --view '{"kind":"graphql-contract","collection":"references","limit":20}' \
-  --evidence_output ./graphql.evidence.json --json
-```
-
-Collections are `types`, `fields`, `definitions`, `references`, `fragment-spreads`
-and `diagnostics`. Each supports `fields`, `offset` and `limit` (default 64).
-Exact batch filters include type/field/definition/reference IDs, type names,
-`field_keys` such as `Query.viewer`, owning type names, binding/spread states
-and diagnostic codes. Filters intersect; an empty array selects nothing.
-Identity, source and applicable uncertainty fields always remain. Retained pages
-and bundle-based queries use the same `graphql-contract` views without rereading
-SDL or rebuilding its schema model.
-
-Types and fields retain individual declaration occurrences, including extensions,
-list/non-null wrappers, implemented interfaces and union member names. Operation
-and fragment definitions own field references with aliases and parent-reference
-IDs. Each reference links to a supplied SDL field occurrence, remains `model-only`
-for a library-provided field such as `__typename`, or records an exact unknown
-reason. Rejected schema construction keeps declarations but cannot supply trusted
-bindings. Missing or duplicate fragment names remain explicit. Fragments are
-visited once in their declared type scope and linked by spread edges; cycles
-are never recursively expanded.
-
-The versioned `graphql-sdl-field-bindings-v1` profile records the GraphQL library
-version. It performs syntax parsing and schema construction for field resolution;
-it does not establish whole-schema/operation validity, spread applicability,
-reachability, authorization or endpoint behavior. Arguments, defaults,
-descriptions, directive behavior, enum value inventory, introspection JSON,
-federation composition and version comparison remain outside this profile.
-
-Every fact has a document role, SHA-256, UTF-16 start/end offsets and parser token
-line/column. Offsets address decoded UTF-8 text, including an optional BOM, rather
-than byte positions. The two files are independently verified snapshots, not an
-atomic pair. Fact IDs identify source occurrences; `field_key` separately supports
-exact name-based joins and does not assert equivalence across revisions. CLI
-retains its auxiliary path spelling in `caller_input_paths.operations_path`,
-outside semantic identity, as well as its primary `caller_input_path`.
-
-Malformed operation text retains the SDL inventory with partial coverage and a
-source-located diagnostic. A primary parser refusal or later resource/cancellation
-failure retains known source identities and available interpreted Evidence;
-syntax diagnostics do not quote source text. Complete Evidence contains facts,
-not original document bytes. An exhausted page never upgrades source coverage.
-
-Each file has the same configurable maximum of 32 MiB. Conservatively charged
-facts share a 32 MiB allowance; text/AST allocation is admitted against available
-heap. The parser admits at most 262,144 lexical tokens and 65,536 comments per
-document; subsequent iterative AST admission limits traversal depth to 128.
-These are REA resource policies, not GraphQL language limits. Very deep input can
-be refused by the parser before AST admission. Selected replies reduce transport
-and retained queries reuse immutable facts; they do not avoid the initial parse.
-
-The committed SWAPI SDL is an unchanged public application fixture with provenance
-in `tests/fixtures/graphql/README.md`. It supplies 53 types and 243 fields;
-verification does not execute its API.
-
-Large complete inventories can exceed the default MCP response budget even when
-selected pages fit. Use `export_evidence_bundle` with a caller-selected local
-path for complete retained Evidence, or CLI complete JSON/bundle publication.
-A transport refusal does not erase a completed retained analysis. Narrow pages
-and source coverage remain available on the same continuing connection.
@@ -174,7 +174,7 @@ OpenJDK 25 against a signed aapt2-built probe APK carrying two resource
 locales — launcher version, on-disk digest agreement, apktool.yml metadata
 (1.2.3, SDK 24–34), manifest package agreement, default and `de` string
 tables projected. Parser goldens in the test suite come from the same
-decode. See `docs/development/testing.md` for the lane summary.
+decode. See `docs/testing.md` for the lane summary.

 Multi-locale and table-only projection were also verified through real CLI and
 stdio MCP workflows on Linux with Apktool 3.0.3/JDK 21 against NewPipe 0.29.1,
@@ -87,7 +87,7 @@ that matches none of those rules is `unclassified`.

 Opened Mach-O and dSYM UUID joins remain unobserved. Symbol names printed
 inside the report are recorded claims and are not verified. Linux ELF cores
-use the separate [recorded crash](guides/native/recorded-crashes.md) workflow.
+use the separate [recorded crash](recorded-crashes.md) workflow.

 ## Limits and failures

@@ -125,7 +125,7 @@ reply budget applies to the decoder record; the CLI/MCP Evidence envelope adds
 copies and encoding overhead. The
 pinned MCP SDK defaults to a 10 MiB receive buffer. Large complete results need
 a caller-configured `StdioClientTransport({ maxBufferSize: ... })` and a matching
-server `REA_MCP_MAX_RESPONSE_BYTES`. See [MCP delivery budgets](../../reference/mcp-contracts.md#tool-results).
+server `REA_MCP_MAX_RESPONSE_BYTES`. See [MCP delivery budgets](mcp-contracts.md#tool-results).
 These settings affect delivery, not decoder coverage or limits. The large
 extended-index verification uses 256 MiB and an explicit five-minute request
 timeout in its separate opt-in MCP lane. REA does not silently truncate the result. Python lowers resource soft limits to at most 3 GiB virtual address space,
@@ -1,62 +0,0 @@
-# Binary hardening
-
-Use `inspect_binary_hardening` to read compile-time and link-time hardening from
-an explicit local ELF, PE, or Mach-O file. No disassembler, pwntools install, or
-target execution is required. Universal Mach-O files return one image per slice.
-
-```sh
-rea inspect-binary-hardening /absolute/path/to/program --json
-rea inspect-binary-hardening /absolute/path/to/program --max-file-bytes 1048576 --json
-```
-
-MCP accepts `{ "path": "/absolute/path/to/program" }`. CLI paths may be relative
-to the current directory; MCP paths must be absolute.
-
-Each image has one row per property: `property`, `state`, `confidence`, `basis`,
-`location`, `note`, and `next_probe`. States are `enabled`, `disabled`,
-`partial`, `unknown`, and `not_applicable`. `confidence` is `observed` for a
-single header or import, and `derived` when the state combines several fields,
-such as ELF PIE or full RELRO. An image's `architecture` is its CPU family, or
-null when REA has no family for it. `machine` and `slice.architecture` keep the
-exact identity, such as `arm64e`.
-
-ELF rows cover PIE (`ET_DYN` with `PT_INTERP` or `DF_1_PIE`), NX (`PT_GNU_STACK`;
-a missing header is `unknown` and the architecture default is only noted), RELRO
-(`PT_GNU_RELRO` plus `BIND_NOW`), stack protector and FORTIFY undefined dynamic
-imports, CET and AArch64 BTI/PAC GNU property notes, `DT_RPATH`, `DT_RUNPATH`, and
-whether a `SHT_SYMTAB` section is present. Only an undefined dynamic import
-counts. Imports come from the table `DT_SYMTAB` declares. A `SHT_DYNSYM` section
-only supplies the symbol count when `DT_HASH` and `DT_GNU_HASH` leave it open,
-and only if it names the same symbol and string tables. Without that count the
-import rows are `unknown` and give the reason. A missing `__stack_chk_fail` or fortify import is `unknown`. That
-absence does not establish that the protection was left out of a static or
-stripped build. A present import is a sign that some code uses the protection,
-not proof that all code does. NX, RELRO, `DT_RPATH`, and `DT_RUNPATH` are
-`not_applicable` when `e_type` is neither `ET_EXEC` nor `ET_DYN`, and `unknown`
-for a linked image with no readable program headers.
-
-PE rows read `DllCharacteristics` for dynamic base, high-entropy VA, NX
-compatibility, force integrity, no SEH, and guard CF. `cfg_instrumented` is the
-load-config `GuardFlags` linker claim when `Size` covers that field. An
-unreadable load configuration, including a TLS failure in that parser, leaves
-only `cfg_instrumented` `unknown`. Authenticode and debug rows report certificate
-and debug directory presence, not signature validity or debug content. A
-directory whose address and size disagree is `unknown`.
-
-Mach-O rows read `MH_PIE`, `MH_ALLOW_STACK_EXECUTION`, `MH_NO_HEAP_EXECUTION`,
-an `__RESTRICT` segment, `LC_CODE_SIGNATURE` presence, encryption from the
-existing encryption reader, the arm64e subtype, and a stack-protector import.
-`hardened_runtime` is `unknown` with `next_probe` `inspect_signature`.
-CodeDirectory flags stay with that tool.
-
-The report states presence of build-time features. It does not state
-exploitability. `inspect_binary_layout` is unchanged.
-
-The default read budget is 64 MiB (`max_file_bytes`, ceiling 512 MiB). A changed
-file is refused. A malformed header, a Mach-O segment or encryption command that fails admission, or a program, section,
-or segment payload declared outside the file returns no partial report, except that one bad slice in a universal Mach-O leaves the other slices. A symbol table or
-symbol name over its budget leaves the import rows `unknown` and keeps the
-header rows. A GNU property note over its budget, or a compressed note section
-that may hold one, leaves the CET and BTI/PAC rows `unknown` and keeps the header
-rows. A dynamic-table budget still fails the ELF report. The image is never
-executed.
@@ -31,7 +31,7 @@ authority are validated independently before selection and connection.

 For a compact route query, select `detail: "summary"` and a
 `view: {kind: "javascript-routes", collection: "routes", limit: 20}`. The
-shared [route inventory](../../javascript-route-inventory.md) preserves source IDs,
+shared [route inventory](javascript-route-inventory.md) preserves source IDs,
 precise locations, partial coverage, and the complete parent Evidence for
 subsequent filtered pages. Static candidates never establish complete application
 coverage or reachability.
@@ -147,7 +147,7 @@ Caller-owned JSON/base64 strings, input parsing and validation, transport
 buffers, garbage-collector behavior, and other runtime memory are outside this
 estimate; the budget does not promise a bound on total process memory.

-Electron `file://` pages use a separate provider and target boundary; see [electron-observation.md](../javascript/electron-observation.md).
+Electron `file://` pages use a separate provider and target boundary; see [electron-observation.md](electron-observation.md).

 ## Provider authorities

@@ -177,7 +177,7 @@ See [the reproduction and Chromium ownership limitation](https://github.com/morl

 Existing static application Evidence and passive web/Electron captures can be
 combined later through
-[JavaScript static/runtime reconciliation](../javascript/javascript-runtime-reconciliation.md).
+[JavaScript static/runtime reconciliation](javascript-runtime-reconciliation.md).

 ## Start a browser

@@ -9,10 +9,7 @@ liveness deadlines. `INPUT_JSON` may be inline JSON or a JSON file path.

 The minimal request contains only browser launch/connect selection, `start_url`,
 and at least one `actions` entry. Launch `headless` defaults to `true` and can
-be set to `false` where the host supports a visible browser. Launched Chromium
-keeps its sandbox; on hosts that cannot provide one, such as root in a
-container, set `REA_BROWSER_NO_SANDBOX=true` for the REA process. Termux on
-Android always launches without it. Navigations follow
+be set to `false` where the host supports a visible browser. Navigations follow
 the destinations named by the scenario and the page's ordinary browser requests,
 and [request steps](#request-steps) send only to the start URL's origin;
 there is no separate origin allowlist. Request steps use a temporary dispatch
@@ -65,14 +65,14 @@ cancellation can still prevent upload.
 that analysis was complete. A successful operation can retain partial analysis,
 unknowns, and limitations. Exit zero is not a security verdict, proof of complete
 coverage, or a policy gate for those findings. Inspect the saved Evidence and
-coverage before making such a decision. See [output and exit status](getting-started/cli.md#output-and-exit-status).
+coverage before making such a decision. See [output and exit status](cli.md#output-and-exit-status).

 A nonzero exit can represent invalid input, unavailable tooling, an unsupported
 host/capability, or another operation failure. Keep the original JSON error (when
 emitted), stderr, and exit code, and use their category/message to diagnose it.
 An early startup failure may leave `analysis.json` empty; do not parse that as
 successful analysis. Select a supported operation or explicitly provision its
-[documented prerequisites](getting-started/installation.md); do not silently switch providers,
+[documented prerequisites](installation.md); do not silently switch providers,
 execute the artifact, or ignore the failure to obtain a green job.

 To exercise the failure path, temporarily set `ARTIFACT_PATH` to
@@ -4,7 +4,7 @@ Use the CLI for a direct inspection or a script. It uses the same application
 workflows and evidence contracts as REA's MCP server. Each CLI invocation is a
 separate process; save results when you want to use them in a later command.
 For a pinned, noninteractive workflow with retained reports, see
-[static analysis in GitHub Actions](../ci-analysis.md).
+[static analysis in GitHub Actions](ci-analysis.md).

 ## Run a command

@@ -19,7 +19,7 @@ Use an extracted application directory or an ASAR as the target. Static
 JavaScript analysis returns the application graph and Evidence directly.
 Generic `rea analyze PATH` selects this workflow for directories and `.asar`
 files when neither `--provider` nor `--snapshot` is supplied. See
-[JavaScript artifact reconstruction](../guides/javascript/javascript-artifact-reconstruction.md)
+[JavaScript artifact reconstruction](javascript-artifact-reconstruction.md)
 for results, integrity checks and coverage.

 The complete application Evidence can be hundreds of megabytes for a real
@@ -39,17 +39,6 @@ pass an absolute path. REA reads and authenticates the file, then projects it
 like retained Evidence, so a large file is bounded by the file reader rather
 than charged as inline input.

-An argument that accepts inline JSON or a JSON file path also accepts `-`, which
-reads the request from standard input, so a generated request needs no
-temporary file:
-
-```bash
-jq -nc '{source: {kind: "evidence-file", path: "app-evidence.json"}, view: {kind: "summary"}}' | rea inspect-analysis-view -
-```
-
-Standard input is read once as a single UTF-8 JSON document without a
-byte-order mark, and it is limited to 8 MiB. Put a larger request in a file.
-
 Local file inspection commands reject empty paths and NUL bytes before resolving
 relative inputs, auxiliary files or output destinations. An empty string never
 selects the working directory; use an explicit `.` when selecting that directory
@@ -59,7 +48,7 @@ For example, a 334 MB Obsidian application Evidence file yields a summary view
 of about 10 KB. Replace the view with
 `{"kind": "page", "collection": "modules", "offset": 0, "limit": 32}` for a
 module page. See
-[JavaScript application workflows](../guides/javascript/javascript-application-workflows.md) for
+[JavaScript application workflows](javascript-application-workflows.md) for
 views, feature traces and comparisons that take the same saved Evidence.

 Add `--timings` to a command to write one JSON timing record to stderr. For
@@ -226,7 +215,7 @@ saving the complete original Evidence in a new bundle. Summary requires that
 explicit destination; existing files are preserved. Later
 `inspect-analysis-view` calls can page the exact parent from the saved bundle
 without reopening the assembly. See
-[CLI summary and saved member rows](../guides/managed/managed-code-analysis.md#cli-summary-and-saved-member-rows)
+[CLI summary and saved member rows](managed-code-analysis.md#cli-summary-and-saved-member-rows)
 for the complete command sequence. Omitted or `--detail complete` retains the
 full inline response.

@@ -234,8 +223,8 @@ Choose the workflow from the artifact's contents rather than its `.exe` or
 `.dll` extension. The managed parser requires PE/CLI metadata; it does not
 unpack .NET single-file hosts or decode IL2CPP. For the image, type and method
 names in a Unity `global-metadata.dat`, use
-[IL2CPP metadata](../il2cpp-metadata.md). NativeAOT method bodies require native
-analysis. See the [managed-code guide](../guides/managed/managed-code-analysis.md)
+[IL2CPP metadata](il2cpp-metadata.md). NativeAOT method bodies require native
+analysis. See the [managed-code guide](managed-code-analysis.md)
 for supported deployment forms, selection semantics, and coverage limits.

 ## SQLite snapshots
@@ -243,7 +232,7 @@ for supported deployment forms, selection semantics, and coverage limits.
 For a local database snapshot, use `rea inspect-sqlite-database PATH --json`.
 Add `--table NAME --row-limit 20` to read a bounded sample from an ordinary
 table. This command does not require a native analysis provider. See
-[SQLite database snapshots](../guides/data/sqlite-databases.md) for database/WAL identity,
+[SQLite database snapshots](sqlite-databases.md) for database/WAL identity,
 source-file handling and row-value semantics.

 ## Native analysis
@@ -256,7 +245,7 @@ rea inspect-go-binary /absolute/path/to/program --json
 ```

 The shared CLI/MCP workflow reports compiler version, modules, replacements,
-build settings, original bytes and SHA-256. See [Go binaries](../guides/native/go-binaries.md)
+build settings, original bytes and SHA-256. See [Go binaries](go-binaries.md)
 for supported containers and absent or malformed metadata.

 Inspect a Godot PCK without running the game:
@@ -267,7 +256,7 @@ rea extract-artifact game.pck --json
 ```

 Formats 2, 3 and 4 retain header, directory and integrity facts. Compact delivery
-keeps complete Evidence in the requested bundle. See [Godot PCK](../godot-pck.md)
+keeps complete Evidence in the requested bundle. See [Godot PCK](godot-pck.md)
 for embedded packs, batch queries and unknown encrypted coverage.

 Inspect a UnityFS AssetBundle without running Unity:
@@ -278,20 +267,9 @@ rea extract-artifact content.bundle --json
 ```

 Format versions 6 through 8 retain header, block and directory facts with
-none/LZ4/LZ4HC block decompression. See [UnityFS](../unityfs.md) for encryption
+none/LZ4/LZ4HC block decompression. See [UnityFS](unityfs.md) for encryption
 and LZMA coverage boundaries.

-Inspect a WeChat mini-program package without WeChat or an unpacker:
-
-```sh
-rea inspect-artifact app.wxapkg --detail summary --evidence_output evidence.json --json
-rea extract-artifact app.wxapkg --json
-```
-
-Plaintext packages retain header, table and member facts with verbatim member
-bytes. `V1MMWX` packages are detected as encrypted coverage and refused on
-extraction. See [wxapkg](../wxapkg.md) for layout and coverage boundaries.
-
 Inspect an ESP32-family app or bootloader image without esptool:

 ```sh
@@ -301,7 +279,7 @@ rea extract-artifact firmware.bin --json

 The inventory lists each segment with its ESP-IDF load classification, the
 checksum and SHA-256 results, the descriptor and any Secure Boot v2 signature
-blocks. See [ESP images](../esp-image.md) for recognition, coverage and refusals.
+blocks. See [ESP images](esp-image.md) for recognition, coverage and refusals.

 Inspect an ESP flash dump, or one read from a flash address other than 0:

@@ -313,7 +291,7 @@ rea extract-artifact flash.bin --json

 The inventory lists the bootloader, the partition table and each partition,
 with ESP image facts for app partitions and the OTA records. See
-[ESP flash images](../esp-flash-image.md) for table location, inputs and limits.
+[ESP flash images](esp-flash-image.md) for table location, inputs and limits.

 Inspect a Node.js SEA carrier without running it:

@@ -322,7 +300,7 @@ rea inspect-artifact ./application --json
 rea extract-artifact ./application --json
 ```

-See [Node.js SEA](../node-sea.md) for supported layouts, script and asset paths,
+See [Node.js SEA](node-sea.md) for supported layouts, script and asset paths,
 fuse observations, and the real-fixture verification lane.

 Inventory and extract Intel HEX or S-record regions:
@@ -332,7 +310,7 @@ rea inspect-artifact ./firmware.hex --json
 rea extract-artifact ./firmware.hex --json
 ```

-See [Intel HEX and S-record images](../hex-records.md) for recognition, region
+See [Intel HEX and S-record images](hex-records.md) for recognition, region
 names, metadata and limits.

 Inspect and extract stored U-Boot legacy uImage payloads and components:
@@ -342,17 +320,14 @@ rea inspect-artifact ./firmware.bin --detail summary --evidence_output firmware.
 rea extract-artifact ./firmware.bin --json
 ```

-See [U-Boot uImage](../uimage.md) for verified CRCs, physical component ranges,
+See [U-Boot uImage](uimage.md) for verified CRCs, physical component ranges,
 unknown names, resource limits and retained views. Compressed bytes stay stored.

 `inspect-artifact` and `extract-artifact` also read ZIP members compressed with
 Zstandard (standard method 93). They retain the shared ZIP CRC, declared-size,
 overlap and archive expansion checks. The native streaming decoder keeps the
 existing 128 MiB Zstandard window cap; frames requiring a larger window are
-reported as a resource limit (`reason: limit`, `boundary: memory`), rather than
-as archive corruption. The cap cannot be raised at runtime: recompress with a
-window of at most 128 MiB, or decompress externally before retrying.
-Deprecated method 20 and other unregistered ZIP codecs remain unsupported.
+refused. Deprecated method 20 and other unregistered ZIP codecs remain unsupported.

 Inventory and extract UF2 or DfuSe regions:

@@ -361,7 +336,7 @@ rea inspect-artifact ./firmware.uf2 --json
 rea extract-artifact ./firmware.dfu --json
 ```

-See [UF2 and DfuSe images](../uf2-dfuse.md) for recognition, families, numbering,
+See [UF2 and DfuSe images](uf2-dfuse.md) for recognition, families, numbering,
 the DfuSe suffix CRC and limits.

 Inventory and extract U-Boot FIT images:
@@ -371,7 +346,7 @@ rea inspect-artifact ./boot.itb --json
 rea extract-artifact ./boot.itb --json
 ```

-See [U-Boot FIT images](../fit-images.md) for recognition, data sources, hashes
+See [U-Boot FIT images](fit-images.md) for recognition, data sources, hashes
 and limits.

 Inspect local model declarations without loading weights:
@@ -385,7 +360,7 @@ Default hashing reads only headers and leaves full-file identity unknown.
 `--hash full` streams the complete file for SHA-256. Both return typed metadata,
 original tensor declarations and derived totals. MCP summaries retain complete
 Evidence for filtered metadata, tensor and type-total pages; CLI compact delivery
-uses `--detail summary --evidence_output FILE`. See [model files](../model-artifacts.md).
+uses `--detail summary --evidence_output FILE`. See [model files](model-artifacts.md).

 Inspect Unity IL2CPP metadata names without Unity or a disassembler:

@@ -402,7 +377,7 @@ method instances and `--ghidra-seeds PATH` then writes Ghidra function seeds. It
 with retained Evidence; query indexed rows with filters, batch indices and
 selected fields. The CLI defaults to complete Evidence;
 `--detail summary --evidence_output FILE` exports the full result to a new file
-and returns a compact overview. See [IL2CPP metadata](../il2cpp-metadata.md).
+and returns a compact overview. See [IL2CPP metadata](il2cpp-metadata.md).

 Inspect an embedded cargo-auditable Rust dependency list without installing
 Rust or configuring a disassembler:
@@ -414,7 +389,7 @@ rea inspect-rust-binary /absolute/path/to/program --json
 The same workflow reports package names, versions, sources, the root package,
 dependency edges, and the section's file range. A missing `.dep-v0` section is
 null metadata, not proof that the binary has no dependencies. See
-[Rust binaries](../rust-binaries.md).
+[Rust binaries](rust-binaries.md).

 Inspect a PE Authenticode certificate table without executing the image or
 verifying signatures:
@@ -426,7 +401,7 @@ rea inspect-pe-certificates /absolute/path/to/application.exe --json
 The workflow reports `WIN_CERTIFICATE` entries and, for PKCS#7 signedData,
 embedded X.509 serial, issuer, subject, and validity fields. A missing security
 directory is observed absence of that table. See
-[PE Authenticode certificate tables](../pe-certificates.md).
+[PE Authenticode certificate tables](pe-certificates.md).

 Inspect PE import and delay-load tables without executing the image:

@@ -437,7 +412,7 @@ rea inspect-pe-imports /absolute/path/to/application.exe --json
 The workflow reports DLL names, named and ordinal functions, delay-load
 descriptors, and a pefile-compatible import hash of the standard import table.
 A missing import directory is observed absence of that table. See
-[PE import and delay-load tables](../pe-imports.md).
+[PE import and delay-load tables](pe-imports.md).

 Inspect ELF PT_NOTE and SHT_NOTE tables without executing the image:

@@ -447,7 +422,7 @@ rea inspect-elf-notes /absolute/path/to/program --json

 The workflow reports note owners, types, descriptor hashes, and GNU build-id
 or ABI-tag fields when those descriptors match. A missing note table is
-observed absence of those declarations. See [ELF note tables](../elf-notes.md).
+observed absence of those declarations. See [ELF note tables](elf-notes.md).

 Inspect an Apple `.ips` crash report without executing a target:

@@ -458,7 +433,7 @@ rea inspect-apple-ips /absolute/path/to/report.ips --json
 The workflow reports first-line metadata, process/exception/termination facts,
 threads, usedImages, lossless integer registers, and documented crash classes
 when `bug_type` is `"309"`. Other DiagnosticReports types return no crash
-result. See [Apple IPS crash reports](../apple-ips.md).
+result. See [Apple IPS crash reports](apple-ips.md).
 Inspect Linux kernel module metadata without executing the module or requiring
 `modinfo`:

@@ -474,10 +449,9 @@ not decoded and the signature is not validated. Other ELF types are not
 applicable. gzip, xz, and zstd containers are unsupported and name
 `external_decompression` as the next probe: decompress with an external
 utility, then inspect the decompressed file. See
-[Linux kernel modules](../kernel-modules.md).
+[Linux kernel modules](kernel-modules.md).

-Inspect a CPython 3.7–3.13 `.pyc` header and nested marshal code objects (3.14 and
-3.15 headers are qualified but their marshal layout is not pinned)
+Inspect a CPython 3.7–3.13 `.pyc` header and nested marshal code objects
 without executing bytecode or installing Python:

 ```bash
@@ -486,7 +460,7 @@ rea inspect-python-pyc /absolute/path/to/module.pyc --json

 The workflow reports the pinned CPython version for the magic, PEP 552 hash or
 mtime/size fields, nested function names, and bytecode SHA-256. Bytecode is
-not decompiled. See [CPython pyc inspection](../python-pyc.md).
+not decompiled. See [CPython pyc inspection](python-pyc.md).

 Inspect an Erlang BEAM file without executing bytecode:

@@ -496,19 +470,10 @@ rea inspect-erlang-beam /absolute/path/to/app.beam --json

 The workflow reports IFF chunk names, atom tables, exports, imports, lambdas,
 and the Code chunk header. Missing optional tables stay null. See
-[Erlang BEAM files](../erlang-beam.md).
-
-Complete `rea decompile --json` Evidence can be saved and inspected through
-`inspect-analysis-view` with an inline source and
-`view: {kind: "native", facet: "pseudocode", offset: 0, limit: 20000}`.
-The projection reads that saved observation without starting a provider;
-offsets/limits count UTF-16 code units. A summary view preserves the original
-selector and distinguishes null from empty text. The MCP tool additionally
-supports `detail: "summary"` on its first call to retain the complete source
-without returning the body inline; see [native investigation](../guides/native/native-investigation.md).
+[Erlang BEAM files](erlang-beam.md).

 Configure [Hopper or Ghidra](installation.md#hopper), the
-[IDA adapter](../providers/ida-provider.md), or [Kuna](../kuna-provider.md) before analyzing a
+[IDA adapter](ida-provider.md), or [Kuna](kuna-provider.md) before analyzing a
 native target. Substitute
 your target, search text and function name or address in these examples:

@@ -536,11 +501,11 @@ MCP `analyze_function` defaults to the same summary and retains the complete
 dossier in the session for `inspect_analysis_view`.

 Run `rea --help` or a command's `--help` for arguments and output options.
-The [generated catalog](../reference/mcp-contracts.md#generated-catalog) lists all CLI commands and MCP
+The [generated catalog](mcp-contracts.md#generated-catalog) lists all CLI commands and MCP
 tools. Provider-specific target support is described in the
-[native guide](../guides/native/native-investigation.md), [DOS guide](../providers/ghidra-dos.md),
-[raw binary guide](../providers/raw-binary.md), [GameCube DOL guide](../ghidra-dol.md), and
-[Windows Ghidra guide](../providers/windows-ghidra-p0.md).
+[native guide](native-investigation.md), [DOS guide](ghidra-dos.md),
+[raw binary guide](raw-binary.md), [GameCube DOL guide](ghidra-dol.md), and
+[Windows Ghidra guide](windows-ghidra-p0.md).

 ## Choose a provider

@@ -587,13 +552,13 @@ For Hopper, Ghidra, IDA, JADX, and Kuna, run
 such as `pwntools-elf`, report their configuration requirements directly and are
 not accepted by `doctor --provider`. See
 [task readiness](installation.md#check-readiness-for-your-task) and
-[provider selection](../reference/mcp-contracts.md#identity-and-discovery).
+[provider selection](mcp-contracts.md#identity-and-discovery).

 The session reports work still in progress through `analysis_activity`.
 A client timeout can end its wait while the provider continues analyzing.
 `cleanup_incomplete` identifies resources whose shutdown or removal could not
-be verified. See [MCP contracts](../reference/mcp-contracts.md) for session lifecycle and
-[Ghidra first-query deadlines](../reference/mcp-contracts.md#ghidra-first-query-deadlines-and-recovery)
+be verified. See [MCP contracts](mcp-contracts.md) for session lifecycle and
+[Ghidra first-query deadlines](mcp-contracts.md#ghidra-first-query-deadlines-and-recovery)
 for import, client timeouts and recovery.

 A one-shot command releases its provider session and REA runtime before it
@@ -664,11 +629,6 @@ rea analyze /absolute/path/to/program --provider ghidra --snapshot /absolute/pat
 ```

 An exact CLI cache hit is normally read before starting a provider process.
-`decompile --provider ghidra --snapshot ...` also retains its single selected
-Program's pseudocode result, even without an explicit document selector. Old
-snapshots that contain only the Evidence need one new query to add that replay
-entry. This does not retain every body from `decompile-all` or make a persistent
-session's implicit document replayable.
 On Windows, Ghidra first admits the selected source through its native snapshot
 owner, so replay can start that provider.
 In MCP, `open_binary` accepts `snapshot_path` to import a snapshot atomically
@@ -721,10 +681,6 @@ results and Evidence. These are cached observations, not a saved provider
 database: only eligible exact queries can reuse a result, and new or live
 queries can still require provider startup. The CLI uses the same snapshot
 format and preserves these records when loading and updating it.
-When an MCP session replays a provider observation, its delivered Evidence identifies
-the original observation through `evidence_links` and reports that the
-provider was not rerun. The original and its available source records remain
-in the investigation bundle.

 ## Import, export and compare Evidence

@@ -742,23 +698,15 @@ rea compare left.json right.json --record_pairs '[{"left_evidence_id":"ev_<left-
 Migration: replace `rea compare-bundles` with `rea compare`; the former command
 has been removed. The MCP tool remains `compare_bundles`.

-`rea evidence-import` performs process-local bundle authentication and
-validation, reporting record and Unknown-revision counts. `unknowns_added`
-counts revisions, not distinct Unknown IDs. It does not retain records in a
-separate or background MCP server process. To retain records across calls in an
-active MCP session, use the MCP tool `import_evidence_bundle` in that session.
-
 `rea compare` compares records by Evidence identity and explicit pairs. It does
 not read artifact contents: the inventories of two builds are unresolved
 records, or one opaque change when you pair them. Use `compare-artifacts`,
 described at the end of this section, to compare their contents.

-`--record_pairs` accepts an inline JSON array or the path to a local JSON
-file containing that array, matching MCP `compare_bundles.record_pairs`. For a
-file, use `rea compare left.json right.json --record_pairs pairs.json --json`.
-Pair IDs must exist on their named sides and be one-to-one. Without pairs,
-one-sided membership remains unknown; REA does not infer correspondence from
-position or display names.
+`--record_pairs` supplies an explicit JSON array of observation pairs, matching
+MCP `compare_bundles.record_pairs`. Pair IDs must exist on their named sides and
+be one-to-one. Without pairs, one-sided membership remains unknown; REA does
+not infer correspondence from position or display names.

 Exports preserve an existing destination unless `--overwrite` is explicit.

@@ -769,8 +717,8 @@ protection still applies. A genuine pathname refusal uses `resource_constraint`
 with `details.reason: path-limit` and `boundary: filesystem-path`.

 For application traces and version comparisons, see
-[JavaScript application workflows](../guides/javascript/javascript-application-workflows.md).
-MCP [retained Evidence references](../reference/mcp-contracts.md#retained-application-evidence-inputs)
+[JavaScript application workflows](javascript-application-workflows.md).
+MCP [retained Evidence references](mcp-contracts.md#retained-application-evidence-inputs)
 belong to one connection. Separate CLI calls can consume full saved records or
 resolve exact retained IDs from an explicitly selected local bundle:

@@ -805,8 +753,7 @@ from the bundle for every supported view kind. Bundles exported from MCP work
 for these commands. Its inline source form cannot also select a bundle.
 A missing ID is refused with `details.reason: "missing"`;
 supplying a bundle does not make incompatible Evidence valid for a workflow.
-`compare-managed-members` keeps its two assembly paths and an optional
-repeatable `--type` selection applied to both sides, and
+`compare-managed-members` keeps its two assembly paths, and
 `compare-process-captures` keeps its two capture Evidence JSON paths. The bundle
 option above selects an input; producer options that write a new bundle, such
 as `inspect-managed-members --evidence-bundle`, retain their existing meaning.
@@ -844,7 +791,6 @@ Import an older source tree to compare with the current artifact:
 ```bash
 rea import-reference-source /absolute/path/to/source
 rea import-reference-source /absolute/path/to/source --detail summary --outline-depth 2 --json
-rea import-reference-source /absolute/path/to/source --exclude-paths '["vendor/","*.generated","!keep.generated"]'
 ```

 The default (`--detail full`) returns the complete `HistoricalSourceGraph`.
@@ -978,23 +924,19 @@ for percent signs, query marks and fragments.
 Historical-source import requires safe no-follow file opens on Linux or
 macOS. Native Windows returns `unsupported_host`; use Linux REA inside WSL
 or another supported host. See
-[source-to-bundle comparison](../guides/javascript/javascript-application-workflows.md#historical-source-to-bundle-comparison)
+[source-to-bundle comparison](javascript-application-workflows.md#historical-source-to-bundle-comparison)
 for mapping identities, inferences and unknowns.

 ## Capture runtime behavior

 Choose the guide for the target and intended interaction:

- [Browser observation](../guides/web/browser-observation.md): inspect a selected page through CDP.
- [Browser scenarios](../guides/web/browser-scenario-contract.md): run declared interactions and capture their results.
- [Electron observation](../guides/javascript/electron-observation.md): inspect an Electron renderer or capture an application scenario.
- [Electron fuses](../electron-fuses.md): read packaged fuse bytes before expecting `--inspect` to reach an Electron main process.
- [Node/Electron Inspector](../guides/javascript/javascript-runtime-observation.md): record script locations and execution contexts.
- [Process capture](../guides/runtime/process-capture.md): run an executable and compare terminal, exit and filesystem observations.
- [Desktop application capture](../desktop-application-capture.md): launch a Linux desktop application and record its windows and home-directory state at checkpoints while it is used.
- [Desktop application state](../desktop-application-state.md): read a capture folder into the application's state files, typed views of each version and kinds of change.
- [Desktop application export](../desktop-application-export.md): write a capture folder as an agentenv computer app bundle with its class, skill and seed.
- [Desktop application tasks](../desktop-application-tasks.md): describe how a capture's files changed, then validate an agent-written task against the capture and export it with its verifier.
+- [Browser observation](browser-observation.md): inspect a selected page through CDP.
+- [Browser scenarios](browser-scenario-contract.md): run declared interactions and capture their results.
+- [Electron observation](electron-observation.md): inspect an Electron renderer or capture an application scenario.
+- [Electron fuses](electron-fuses.md): read packaged fuse bytes before expecting `--inspect` to reach an Electron main process.
+- [Node/Electron Inspector](javascript-runtime-observation.md): record script locations and execution contexts.
+- [Process capture](process-capture.md): run an executable and compare terminal, exit and filesystem observations.

 Runtime requests name the target and actions. Launched targets run with your
 user permissions; consult the chosen guide for host requirements and effects.
@@ -1033,7 +975,7 @@ one client at a time: a session ends with the client's `DELETE`, and a client
 that connects while another session is open takes it over, so a client that
 exited without ending its session needs no restart. The listener runs until
 SIGINT or SIGTERM and does not stop when stdin closes. See
-[transports](../reference/mcp-contracts.md#transports) for the session, `Host` header and
+[transports](mcp-contracts.md#transports) for the session, `Host` header and
 shutdown contract. Client registrations written by setup and the MCP registry
 entry keep stdio.

@@ -1058,7 +1000,7 @@ answers every method with JSON-RPC `-32601`. The stopped document's `state`
 member is `{"served": true, "evidence_id": …}`,
 `{"served": false, "reason": "replay-only"}` or
 `{"served": false, "reason": "unavailable", "code": …, "message": …}`; see
-[serve from the state](../agent-environments.md#serve-from-the-state).
+[serve from the state](agent-environments.md#serve-from-the-state).

 ```sh
 rea environment-serve manifest.json --evidence capture.json --port 8765
@@ -1078,7 +1020,7 @@ MCP_ALLOWED_HOSTS=127.0.0.1,rea.lan rea environment-serve manifest.json --eviden
 the served environment; set but blank, it is refused as `configuration_invalid`
 like a blank `MCP_HOST`. The admitted client URL is written to stderr as one JSON log line
 (`"msg":"MCP transport listening"`). See
-[agent environments](../agent-environments.md) for what the state and replay
+[agent environments](agent-environments.md) for what the state and replay
 return and do not establish.

 ## Build an environment bundle
@@ -1103,7 +1045,7 @@ command. `--dry-run` writes nothing and may omit the directory.
 rea environment-build grafana.har ./grafana --json
 ```

-See [agent environments](../agent-environments.md#build-a-bundle-in-one-step)
+See [agent environments](agent-environments.md#build-a-bundle-in-one-step)
 for the report, the hints and what the bundle ships.

 ## Export an environment bundle
@@ -1136,7 +1078,7 @@ name Windows reserves (`con`, `nul`, `com1` and the like) is refused. The
 command prints one JSON document listing the written files with their sizes,
 the pinned package source, the served `tool_count`, and `state` in the shape
 of the serve command's stopped document. See
-[agent environments](../agent-environments.md#export-a-bundle) for the folder
+[agent environments](agent-environments.md#export-a-bundle) for the folder
 layout and what the smoke task checks.

 ## Compare an environment with its application
@@ -1149,7 +1091,7 @@ answer is compared with the application's after ids are mapped and clocks and ge
 makes no network call. It prints the report and exits `0`, or prints a structured `invalid_request` error and exits `1`
 for the same pair refusals as `environment-serve`, a probe that is not capture Evidence, or a browser probe captured
 without response bodies, or without the request bodies its writes need. See
-[agent environments](../agent-environments.md#measure-fidelity-against-the-application) for the report.
+[agent environments](agent-environments.md#measure-fidelity-against-the-application) for the report.

 ```sh
 rea environment-compare manifest.json --evidence capture.json --probe probe.json --json
@@ -1206,10 +1148,6 @@ such as `UNSUPPORTED_OUTPUT_COMBINATION` for `--json` with `--token-limit`. Use
 Commands reject surplus positional arguments before execution, including commands
 that accept no positionals. Use `rea <command> --help` for the declared argument
 shape; a final variadic argument continues to accept multiple values.
-`rea mcp add` accepts options only and rejects unknown options before reading or
-backing up client settings or starting registration. Its `--agent` and
-`--command`/`-c` options accept spaced and equals forms. Values must be nonempty; a following flag does not satisfy a spaced option's
-missing value.

 `rea mcp doctor --json` checks production MCP startup and reports child logs in
 `diagnostics`. It drains stderr while retaining at most its first 64 KiB of raw
@@ -1250,12 +1188,9 @@ treated as malformed.
 exact array path with `--filter-output` and provide comma-separated direct
 scalar columns with `--columns`; column order is the output column order:

-For an artifact inventory request that selects the `occurrences` collection
-and includes `logical_path` and `artifact_id` in its view fields:
-
 ```bash
 rea inspect-analysis-view request.json --format csv \
-  --filter-output normalized_result.items --columns logical_path,artifact_id
+  --filter-output normalized_result.rows --columns name,address
 ```

 The first line is a REA metadata record,
@@ -1350,9 +1285,7 @@ the command's signal handling. Commands routed through the shared
 `withCommandCancellation` handler in the CLI set status `130` for SIGINT or
 `143` for SIGTERM after their operation settles. Current source registrations
 use that handler for process capture and comparison (`capture-process`,
-`compare-process-captures`), desktop application capture and state
-(`capture-desktop-application`, `inspect-desktop-application-state`,
-`export-desktop-application`, `describe-desktop-application-task`), JavaScript application analysis (`analyze` when it
+`compare-process-captures`), JavaScript application analysis (`analyze` when it
 selects the JavaScript lane, and `analyze-javascript-application`), selected
 browser, web and Electron commands (including `analyze-web-bundle`,
 `observe-web-execution`, `capture-browser-scenario` and
@@ -1398,11 +1331,7 @@ status with the analysis failure status, so it exits `1`. Setup has its own cont
 structured result and process status as separate signals when scripting
 cancellation.

-`setup --dry-run` returns `planned` and exits `0`. For `setup` and
-`environment-build`, explicit `--dry-run=true` and `--dry-run=false` are
-accepted; empty or other values fail with `PARSE_ERROR` before any changes.
-Every supplied value is checked even when a later occurrence overrides it.
-A cancelled setup also exits
+`setup --dry-run` returns `planned` and exits `0`; a cancelled setup also exits
 `0`. Setup returns `1` for `needs_confirmation` or `needs_human`.
 `doctor` returns `1` when required checks in its selected readiness scope fail;
 unavailable optional providers remain informational for unrelated tasks.
@@ -1429,7 +1358,7 @@ the total token count and have no next offset.

 Inspect an explicit local FDT v16/v17 blob without execution or an external tool.
 Returns header, reservations, node/property tree, derived standard values and
-selected phandle references. See [devicetree inspection](../devicetree.md) for
+selected phandle references. See [devicetree inspection](devicetree.md) for
 limits and retained-view pagination.

 ```bash
@@ -1445,19 +1374,9 @@ rea inspect-pe-load-config /absolute/path/to/application.exe --json

 Reports TLS callbacks and size-covered load-config fields without execution.
 Use `--max-callbacks` and `--max-file-bytes` to set read budgets. See
-[PE TLS and load configuration](../pe-load-config.md).
-
-### Binary hardening
-
-```sh
-rea inspect-binary-hardening /absolute/path/to/program --json
-```
-
-Reports ELF, PE, and Mach-O hardening rows without execution. A missing import
-is `unknown`, not `disabled`. Use `--max-file-bytes` to set the read budget. See
-[binary hardening](../binary-hardening.md).
+[PE TLS and load configuration](pe-load-config.md).

 Bun standalone executables use the existing `inspect-artifact` and
 `extract-artifact` commands to inventory and materialize embedded source,
 sourcemaps and bytecode without running the executable. See
-[Bun standalone executables](../bun-standalone.md) for layout coverage and limits.
+[Bun standalone executables](bun-standalone.md) for layout coverage and limits.
@@ -24,8 +24,8 @@ the registration uses them. Clearing either makes startup fail without resolving
 another package from the client's project. Restore the same installation before
 repairing it; an unidentified registration remains untouched. See
 [installation and recovery](installation.md#package-runners-and-global-installation).
-Setup forwards supported, explicitly selected REA settings into client
-configuration, but does not copy unrelated ambient environment values. To refresh an older registration, preview
+Setup does not copy your ambient environment into client
+settings. To refresh an older registration, preview
 `rea setup --client <client-id> --skill=false --dry-run`, then run the same command
 without `--dry-run` and approve the displayed changes. Setup preserves unrelated
 settings, backs up changed configuration and leaves an aligned registration
@@ -43,37 +43,12 @@ Rerun setup to review the registration and restart the client.
 executable and environment of the terminal running doctor. It does not launch
 the client's configured command or reproduce the client's environment. If doctor
 passes but the client disconnects, inspect the client's startup error and registered
-launcher; see [verification scope](../development/client-verification.md#launch-environment-verification).
+launcher; see [verification scope](client-verification.md#launch-environment-verification).

 `rea doctor` has the same limit for provider checks, and reports a provider setting
 the registration's file does not carry as a
 [non-blocking unknown](installation.md#check-readiness-for-your-task).

-## Setting launch variables in PowerShell
-
-Shell examples that prefix a command with `REA_MCP_INPUT_SCHEMA_PROFILE=compact`
-use POSIX shell syntax. In PowerShell, set the process environment before
-launching REA:
-
-```powershell
-$env:REA_MCP_INPUT_SCHEMA_PROFILE = "compact"
-rea mcp doctor --json
-```
-
-The assignment applies to the current PowerShell process and commands it launches.
-Restore the previous value when finished, or use
-`Remove-Item Env:REA_MCP_INPUT_SCHEMA_PROFILE` if it was previously unset. It does
-not update an already running MCP server or desktop client.
-
-To select this profile for an agent, set `REA_MCP_INPUT_SCHEMA_PROFILE` in that
-client's existing REA registration `env` object (`environment` for OpenCode) and
-restart the client, preserving its other settings. A successful terminal doctor run does not verify the client's
-launch environment. See [launch-environment verification](../development/client-verification.md#launch-environment-verification)
-and the client-specific instructions below. REA setup forwards supported selections,
-including `REA_MCP_INPUT_SCHEMA_PROFILE`, from its environment into the registration;
-it does not copy unrelated environment values. Restoring the shell's previous
-value does not undo a selection already saved by setup.
-
 ## Runtime settings and client deadlines

 `update_analysis_settings` changes curated defaults inside the running REA
@@ -83,7 +58,7 @@ raising a REA startup or operation deadline, separately ensure the client allows
 enough time for the full request. Use `inspect_analysis_settings` for the running
 server's defaults; `rea doctor` checks launch configuration and cannot observe
 another process's runtime overrides. See the
-[settings design](../design/limits-and-recovery.md) for ownership and lifetime.
+[settings design](design/limits-and-recovery.md) for ownership and lifetime.

 ## Client tool names and discovery

@@ -102,86 +77,11 @@ does not repair a client's naming behavior or infer permission drift from an
 unfamiliar prefix. The unavailable fork reported in
 [#5512](https://github.com/morluto/rea/issues/5512) has not been reverified.

-<a id="hotcold-catalogs"></a>
-
-## Hot/cold catalogs
-
-For a client that supports MCP catalog refresh, set
-`REA_MCP_TOOL_CATALOG_PROFILE=hot-cold` in REA's server environment and restart
-the connection. REA then advertises a small initial catalog and loads other
-named tools through `discover_tools`. Setup preserves this explicit setting.
-See the [discovery contract](../reference/mcp-contracts.md#hotcold-catalog-discovery) for
-pagination, identity and family-scope semantics.
-
-Analysis tools, including `inspect_analysis_view`, load on demand. For example,
-load `inspect_api_contract` and supply its `view` to answer an initial OpenAPI
-or GraphQL question directly. When later questions need retained facts, load
-`inspect_analysis_view` and use the complete `parent_evidence_id`; source files
-need not be reopened. If both tools are needed from the start, request both
-names in one `discover_tools` batch to avoid another catalog refresh. The same
-pattern applies to selected Playwright trace and endpoint-comparison results.
-This defers unused schema delivery and client validator preparation; it does
-not reduce parsing work, alter Evidence or shorten requested facts. Clients
-without catalog refresh should keep the default `full` profile.
-
-Codex CLI 0.165.0 requires its experimental `mcp_tool_list_changed` feature for
-this workflow. Merge these entries into the existing `~/.codex/config.toml`
-without replacing other feature or REA settings:
-
-```toml
-[features]
-mcp_tool_list_changed = true
-
-[mcp_servers.rea.env]
-REA_MCP_TOOL_CATALOG_PROFILE = "hot-cold"
-```
-
-The server setting alone does not enable client refresh. If a successful
-discovery call is followed by a missing tool, check the client's refresh feature
-and tool allow/deny lists. Clients without refresh should use the default
-`REA_MCP_TOOL_CATALOG_PROFILE=full`; reconnect after changing it. The
-[FastMCP HTTP trial](#fastmcp-and-unsloth-sse-catalog-limits) below covers
-explicit refreshes; other clients' automatic refresh remains unverified.
-
-## FastMCP and Unsloth SSE catalog limits
-
-If an HTTP client reports `Server-sent event exceeded the 1048576 byte limit`
-during `tools/list`, merge these settings into the **REA server process's**
-environment, then reconnect:
-
-```text
-REA_MCP_INPUT_SCHEMA_PROFILE=compact
-REA_MCP_OUTPUT_SCHEMA_PROFILE=compact
-REA_MCP_TOOL_CATALOG_PROFILE=full
-```
-
-This advertises all tools without requiring catalog refresh. Compact output
-schemas widen client-side validation; REA still validates complete results
-against the canonical contracts. See [output schemas](../reference/mcp-contracts.md#output-schemas).
-
-On main `3e0599a94`, a real FastMCP 4.1.6 / Python MCP 2.3.0 HTTP client with
-the default 1 MiB SSE event limit rejected the 4,108,975-byte full catalog.
-The settings above delivered all 240 tools in 611,305 bytes and a
-`binary_session` call succeeded. These are measured SSE response sizes for
-that catalog, not a size guarantee for future catalogs or other profiles.
-
-For a client that refreshes tools, combine `hot-cold` with the compact schema
-settings to reduce initial context further: the same trial delivered six
-initial tools in 33,903 bytes, then explicitly refreshed through 34 loaded
-tools. Hot/cold alone later exceeded the SSE limit during refresh. Follow
-the [refresh requirements](#hotcold-catalogs).
-
-The Unsloth report [#9093](https://github.com/morluto/rea/issues/9093) fails at
-catalog delivery; the Unsloth application itself was not exercised in this
-trial. Schema compaction does not bound analysis results. Continue to use
-summary/detail selection and tool-specific paging for larger results; client
-receive limits and full Evidence access still apply.
-
 ## Fiddler Everywhere alongside REA

 Connect Fiddler Everywhere's MCP server separately for HTTP traffic debugging,
 preserving your REA client entry. See the
-[setup instructions and public skills](../guides/web/web-network-captures.md#fiddler-everywhere-mcp-and-public-skills).
+[setup instructions and public skills](web-network-captures.md#fiddler-everywhere-mcp-and-public-skills).

 ## VS Code

@@ -219,7 +119,7 @@ tool inventory on Linux using a loopback model fixture. After setup, add
 settings, then restart the client. Compact advertisements can reduce nested
 schema constraints; REA still validates complete canonical inputs. Full-profile
 `gpt-5.4` metadata is also verified locally. Live model API acceptance and
-Windows remain unverified; see [native client verification](../development/testing.md).
+Windows remain unverified; see [native client verification](testing.md).

 ## Claude Desktop

@@ -230,7 +130,7 @@ in the file the installed app reads:

 - Without Claude Desktop's MSIX package storage, setup uses
  `%APPDATA%\Claude\claude_desktop_config.json`.
- The legacy MSIX storage layout (package family `Claude_pzs8sxrjxfjjc`, installed under
+- The MSIX build (package family `Claude_pzs8sxrjxfjjc`, installed under
  `C:\Program Files\WindowsApps\Claude_<version>_x64__pzs8sxrjxfjjc`)
  virtualizes AppData writes. Once it has saved its configuration, it reads
  the package-private copy
@@ -239,11 +139,6 @@ in the file the installed app reads:
  private copy when it exists. Before the package has saved one, they use the
  `%APPDATA%` file it still reads; with neither file, setup creates the
  private copy.
- If `%LOCALAPPDATA%\Claude-Data\claude_pzs8sxrjxfjjc` exists, setup, doctor
-  and uninstall report an unresolved location. Migrated MSIX installations
-  have been observed reading `claude_desktop_config.json` in this directory.
-  Quit Claude Desktop and verify its active configuration before registering
-  manually. See [#8968](https://github.com/morluto/rea/issues/8968).
 - If `%LOCALAPPDATA%\Packages` holds a `Claude_<publisher ID>` package from
  another publisher, an `AnthropicPBC.Claude_<publisher ID>` package, or cannot
  be read, REA cannot establish which file Claude
@@ -331,7 +226,7 @@ and Claude Code reports that autocompact is thrashing. To avoid this:
  override.
 - To remove entire tool families from the upfront catalog, run
  `rea setup --client claude_code --tool-families <ids>` with the families the
-  workflow needs (see [the advertising scope contract](../reference/mcp-contracts.md#tool-family-advertising-scope)).
+  workflow needs (see [the advertising scope contract](mcp-contracts.md#tool-family-advertising-scope)).
  Out-of-scope tools are not advertised and their calls fail with the SDK's
  disabled-tool error, so widen the selection when a task needs another
  family. Setup writes the scope into the entry's `env` as
@@ -348,7 +243,7 @@ Both keep canonical result validation and complete structured results; `compact`
 keeps a widened root shape and `off` advertises nothing. On catalogs large
 enough that full input schemas alone approach the frame limit, also keep the
 input profile at its `compact` default. See [MCP output schema
-profiles](../reference/mcp-contracts.md#output-schemas).
+profiles](mcp-contracts.md#output-schemas).

 ## Kimi Code

@@ -382,7 +277,7 @@ This headroom is a practical default, not a guarantee for every analysis
 duration. Setup preserves positive timeout values already in the `rea` entry.

 Setup also forwards explicitly selected input/output schema profiles,
-`REA_MCP_MAX_RESPONSE_BYTES`, `REA_MCP_MAX_INPUT_ELEMENTS`, the Windows ChangeTime settle settings `REA_WINDOWS_CHANGE_TIME_DRIFT_MS`, `REA_WINDOWS_CHANGE_TIME_SETTLE_POLL_MS`, and `REA_WINDOWS_CHANGE_TIME_SETTLE_MAX_POLLS`, provider paths and supported Ghidra, JADX and Kuna
+`REA_MCP_MAX_RESPONSE_BYTES`, `REA_MCP_MAX_INPUT_ELEMENTS`, provider paths and supported Ghidra, JADX and Kuna
 settings. It also forwards explicit executable and resource selections for ADB,
 apktool, packet capture, GDB/Rizin/objdump, Cutter, WABT, Wakaru, firmware and
 signal tools, browser inspection, and pwntools/pwndbg. This includes their
@@ -393,7 +288,7 @@ doctor reports its readiness separately. Explicit selections override discovered
 defaults, including when setup runs again with a changed selection. Unrelated
 environment variables, process ownership tokens and one-shot target paths are not
 copied. For an explicitly configured startup target, see the
-[initial-target settings](../reference/mcp-contracts.md#initial-target-at-startup). Existing
+[initial-target settings](mcp-contracts.md#initial-target-at-startup). Existing
 client environment overrides remain intact unless setup supplies the same key.
 You can edit `startupTimeoutMs` and `toolTimeoutMs` there; doctor keeps positive
 caller-selected values aligned and reports a non-blocking advisory when a tool
@@ -415,22 +310,6 @@ Kimi Code also discovers personal skills in `~/.agents/skills` and project-local
 and verifies the matching skill files through the normal shared-skill flow.
 Start a new Kimi Code session to pick up MCP and skill changes.

-## LM Studio
-
-For [LM Studio](https://lmstudio.ai/docs/app/mcp), setup writes `mcpServers.rea`
-into `mcp.json` in the LM Studio home directory. Setup finds that directory as
-LM Studio does: the path stored in `~/.lmstudio-home-pointer`, otherwise
-`~/.cache/lm-studio` when it exists, otherwise `~/.lmstudio`. Setup only reads
-the pointer file. LM Studio parses `mcp.json` as strict JSON, so setup rejects
-a file with comments, trailing commas, or a byte order mark without a backup
-or a write. The entry carries `command`, `args`, and `env`, and setup keeps
-every other server. Local models often have small context windows, so setup
-selects `REA_MCP_INPUT_SCHEMA_PROFILE=compact` unless the stored entry or the
-setup environment selects a profile explicitly. Doctor reports an entry with no
-explicit profile as stale, as for Kimi Code. LM Studio 0.4.26 on macOS loaded
-this registration, and a local model called an REA tool through it. Linux and
-Windows remain unverified.
-
 ## Pi

 For [Pi](https://github.com/earendil-works/pi/blob/main/packages/coding-agent/docs/mcp.md),
@@ -504,7 +383,7 @@ standalone CLI check.
 A model API's `400 INVALID_ARGUMENT` alone does not identify a rejected schema,
 tool-count limit or skill defect. Preserve the response's parameter path and
 diagnostic, the actual running REA version, Gemini CLI version and selected
-model. For schema rejection, review the [input presentation profiles](../reference/mcp-contracts.md#compact-input-schema-profile)
+model. For schema rejection, review the [input presentation profiles](mcp-contracts.md#compact-input-schema-profile)
 and reconnect after changing REA's registration environment. Compact is the
 current default; an explicitly stored `full` choice is preserved. The generic
 error in [#4620](https://github.com/morluto/rea/issues/4620) does not establish
@@ -585,7 +464,7 @@ Responses-compatible Kimi gateway as “infinite recursion”; expanding those
 references succeeded. A separate full-profile input failed the provider's
 schema-size limit. These are distinct reported failures, not proof that the
 canonical schema is recursive. Current REA inputs are already self-contained;
-see [schema advertisement](../reference/mcp-contracts.md#schema-advertisement).
+see [schema advertisement](mcp-contracts.md#schema-advertisement).

 For this failure, inspect the active MCP launch command and refresh the REA
 installation that command actually runs. A configured package selector or the
@@ -711,18 +590,6 @@ The user-level MCP paths follow the editor's VS Code layout. Trae's official
 documentation describes the raw JSON editor without specifying those paths;
 loading this registration in Trae remains unverified.

-## CodeBuddy
-
-For CodeBuddy, setup writes `mcpServers.rea` into the global
-`~/.codebuddy/mcp.json` (a standard `mcpServers` JSON file at the user home
-root on every platform). Entries carry `command`, `args`, and `env`; stdio is
-the default transport. CodeBuddy discovers personal skills from
-`~/.codebuddy/skills`, so setup installs its skill copy there.
-
-The global MCP path is a plain JSON file; setup preserves every other server
-and top-level key when it upserts `rea`. Loading this registration, the
-bundled skill, and real REA tool calls through CodeBuddy are verified.
-
 ## WorkBuddy

 For [WorkBuddy](https://www.workbuddy.cn/docs/workbuddy/From-Beginner-to-Expert-Guide/Function-Description/MCP-Guide), setup writes `mcpServers.rea` into the
@@ -765,20 +632,21 @@ writing a registration ZCode cannot load.

 ## FreeBuff

-For FreeBuff, `rea setup --client freebuff` writes `mcpServers.rea` into the
-user-scope `~/.agents/mcp.json` shared-agent file. Entries carry `command`,
-`args`, and `env`; stdio is the default transport. The personal skill location
-is `~/.agents/skills`, so setup installs its skill copy there. Because the same
+For FreeBuff, the proposed integration writes `mcpServers.rea` into the user-scope
+`~/.agents/mcp.json` shared-agent file. Entries carry `command`, `args`, and
+`env`; stdio is the default transport. The proposed personal skill location is
+`~/.agents/skills`, so setup installs its skill copy there. Because the same
 file doubles as ZCode's user-scope fallback (see above), a `freebuff`
-registration is also in the file ZCode uses until ZCode defines its own native
-server. Setup and doctor detect FreeBuff from its own profile directory
-(`~/.config/freebuff-desktop`), not from the shared `.agents` folder that REA's
-skill installs create for every client.
+registration is also in the file ZCode uses until ZCode defines its own native server.
+Setup and doctor detect FreeBuff from its own profile directory
+(`~/.config/freebuff-desktop`), not from the shared `.agents` folder that
+REA's skill installs create for every client.

-FreeBuff MCP loading and skill discovery have not been verified with an
-installed native FreeBuff client/version; filesystem tests cover REA's editing,
-discovery, and ownership behavior only. Automatic applicability requires the
-FreeBuff profile directory even when the shared MCP file exists.
+The configuration write and personal skill locations are proposed integration
+boundaries. FreeBuff MCP loading and skill discovery have not been verified
+with an installed native FreeBuff client/version; filesystem tests cover REA's
+editing, discovery, and ownership behavior only. Automatic applicability
+requires the FreeBuff profile directory even when the shared MCP file exists.
 When uninstall cannot establish FreeBuff or another shared-storage reader from
 product discovery, a malformed or unreadable shared MCP file is retained
 unchanged and does not stop other REA removals, including `--purge-data`. When
@@ -786,9 +654,8 @@ FreeBuff or ZCode product applicability is established or unresolved, the same
 malformed shared file stops uninstall before removals. See
 [Diagnose, update, and remove](installation.md#diagnose-update-and-remove).

-FreeBuff setup support requires `[email protected]` or later (including the
-current npm `latest` release). Older versions reject
-`rea setup --client freebuff` as an unsupported client. See the
+FreeBuff setup support requires `[email protected]` or later. Older versions
+reject `rea setup --client freebuff` as an unsupported client. See the
 [installation guide](installation.md#supported-agents) for client availability.

 ## DeepSeek Harness
@@ -834,110 +701,13 @@ in `~/.agents/skills` (`$DSH_AGENTS_HOME/skills` when configured); Harness
 discovers that directory, and its native `skill` tool can load
 `reverse-engineer-anything`.

-REA's optional [native client verification](../development/testing.md#end-to-end-integration-and-golden-evidence)
+REA's optional [native client verification](testing.md#end-to-end-integration-and-golden-evidence)
 checks headless chat, skill loading, all tool input schemas and actual analysis
 using the installed Harness and a local model fixture. This establishes the
 Harness integration, with live DeepSeek API compatibility remaining unverified.
 See the [Harness MCP guide](https://github.com/deepseek-ai/deepseek-harness/blob/639ed015397290b3745d163aafe02ffee4aa3f84/packages/mcp/mcp-client/README.md)
 for its native configuration contract.

-<a id="llamacpp"></a>
-
-## llama.cpp
-
-Use REA from llama.cpp's local Web UI through `llama-server`'s native stdio
-MCP support. REA supplies the analysis tools; llama.cpp runs your chosen model.
-It is not a replacement for a native analysis provider such as Ghidra or Hopper.
-
-Install REA in a persistent location so the configuration below can use a stable
-entrypoint. For a project-local installation, run this in your chosen directory:
-
-```bash
-npm install --save-exact rea-agents
-```
-
-Or install it globally:
-
-```bash
-npm install --global rea-agents
-```
-
-See [package runners and global installation](installation.md#package-runners-and-global-installation)
-for runtime requirements and installation options. Running `npx rea-agents setup`
-alone does not create either installation; do not use its temporary package-cache path.
-Use a llama.cpp build whose `llama-server --help` lists
-`--mcp-servers-config`; older builds without that option cannot use this route.
-The configuration below uses an already installed REA package, so tool discovery
-does not depend on downloading an npm package during server startup.
-
-Save a JSON file, for example `rea-mcp.json`:
-
-```json
-{
-  "mcpServers": {
-    "rea": {
-      "command": "/absolute/path/to/node",
-      "args": ["/absolute/path/to/rea-agents/scripts/rea.mjs", "mcp"],
-      "timeout_ms": 450000
-    }
-  }
-}
-```
-
-Replace both paths with your installation's actual paths. For a project-local npm
-installation, run `npm root` in that project; the script is under
-`$(npm root)/rea-agents/scripts/rea.mjs`. For a global installation, use
-`$(npm root -g)/rea-agents/scripts/rea.mjs` instead. Write the resulting absolute
-paths as JSON strings; llama-server does not expand shell expressions there.
-On Windows, use forward slashes, such as `"C:/Program Files/nodejs/node.exe"`,
-or double each backslash, as in `"C:\\Program Files\\nodejs\\node.exe"`.
-Apply this to both `command` and the script path in `args`. Single backslashes
-can make the JSON invalid or change the path through escape sequences.
-`node -p "JSON.stringify(process.execPath)"` prints your current Node.js executable
-as a quoted, escaped JSON string that can be used as the `command` value.
-Use the version supported by REA. Preserve any other
-servers if you are adding REA to an existing configuration. `timeout_ms` is
-llama.cpp's per-tool-call timeout, including cold engine startup. The example
-allows REA's default 330-second Ghidra startup budget plus 120 seconds for the
-operation. Increase it if you configure a longer provider allowance or need more
-operation time; see [provider deadlines](../reference/mcp-contracts.md#ghidra-first-query-deadlines-and-recovery).
-
-Start the server with your own tool-capable GGUF model:
-
-```bash
-llama-server -m /absolute/path/to/model.gguf \
-  --host 127.0.0.1 --port 8080 --parallel 1 --ctx-size 16384 \
-  --mcp-servers-config /absolute/path/to/rea-mcp.json
-```
-
-Open `http://127.0.0.1:8080`. REA tools appear with a `rea_` prefix, such as
-`rea_analyze_javascript_application`. Select only the tools needed for the
-conversation in the Web UI's tool settings: discovery of REA's complete catalog
-does not mean that its schemas and results fit the selected model's context.
-Choose a context size your model and machine support. For a first check, enable
-`rea_analyze_javascript_application` and ask it to inspect a small JavaScript
-directory you own. This task needs no native analysis engine. Inspect the
-returned Evidence and limitations rather than relying only on the model's summary.
-
-If the model prints a proposed call as ordinary text, REA has not been called.
-Check the selected model and its chat template against llama.cpp's function-calling
-guidance. A working MCP connection does not establish reliable tool selection by
-every model.
-
-`--tools all` is not needed; it enables llama.cpp's separate built-in tools.
-`--ui-mcp-proxy` is also not needed for this server-side stdio connection.
-REA's setup wizard does not register llama.cpp automatically; pass the JSON
-file to llama-server explicitly and restart it after changes.
-
-The MCP child runs with llama-server's permissions. Loopback binding does not
-sandbox it or make every REA operation read-only. Enable only trusted commands,
-keep the server local, and select targets and operations you are authorized to use.
-
-See llama.cpp's [MCP server configuration](https://github.com/ggml-org/llama.cpp/blob/master/tools/server/README.md#mcp-servers)
-and [function-calling guidance](https://github.com/ggml-org/llama.cpp/blob/master/docs/function-calling.md).
-The [verification record](../development/client-verification.md#llamacpp) distinguishes connection
-checks from model behavior and lists the tested versions.
-
 ## Other client settings

 For OpenCode, setup writes the V1 `mcp.rea` entry, which OpenCode V1 and V2
@@ -19,7 +19,7 @@ initialization, discovery and target-free request flow; it does not verify a
 client's configured launcher or its inherited environment. Test the generated
 registration through the actual client, including a reduced `PATH` when checking
 desktop or service startup. Record the client version and launch environment
-separately from terminal doctor results. See [launcher troubleshooting](../getting-started/client-configuration.md#launchers-and-path).
+separately from terminal doctor results. See [launcher troubleshooting](client-configuration.md#launchers-and-path).

 ## Published Pi code-mode renderer limit

@@ -33,7 +33,7 @@ shared form would leave later fields unknown instead. The existing
 its character limit by advertising reduced nested validation structure, while
 REA continues to validate calls against the complete canonical input schema.
 Compact is the default for the server's advertised inputs; an explicit `full`
-choice is preserved. See the [compact input schema profile](../reference/mcp-contracts.md#compact-input-schema-profile)
+choice is preserved. See the [compact input schema profile](mcp-contracts.md#compact-input-schema-profile)
 for details of its reduced forms.

 Custom renderer hosts can raise `inputMaxChars` through `renderToolSignature` or
@@ -43,30 +43,6 @@ does not establish broader Pi compatibility. See the pinned upstream
 [`declarations.ts`](https://github.com/earendil-works/pi/blob/b45e0ebcc5ae2fc42a6f2f23104d10e656e6bedb/packages/codemode/src/declarations.ts)
 and [renderer usage notes](https://github.com/earendil-works/pi/blob/b45e0ebcc5ae2fc42a6f2f23104d10e656e6bedb/packages/codemode/README.md#declarations-for-the-model).

-<a id="llamacpp"></a>
-
-## llama.cpp
-
-The [manual stdio connection](../getting-started/client-configuration.md#llamacpp) was checked on
-macOS arm64 with Node.js 24.18.0, llama-server b11715 (`9d1878a43`), and the
-published `[email protected]` package. `GET /tools` exposed 207 REA tools without
-enabling llama.cpp's built-in tools. With the source checkout at `9e372c6`, all
-207 forwarded names, descriptions and input schemas matched a direct MCP client.
-
-Calls through `POST /tools` returned session metadata and JavaScript analysis
-Evidence for a fixture at a Unicode path. A missing target returned REA's input
-error, and a subsequent session call still succeeded. The owned llama-server
-process exited successfully after the checks. No native analysis engine or
-Windows host was exercised.
-
-A local Qwen3-1.7B Q8_0 run selected the JavaScript analysis tool and received its
-Evidence, but its follow-up answer reached the output-token limit. Other small
-Qwen3 attempts returned proposed calls as ordinary JSON text rather than tool
-calls. These runs do not establish dependable model-driven investigations.
-A request with the full catalog and task history exceeded a 16,384-token context;
-select tools for the task instead of assuming that discovery implies model fit.
-The checks exercised HTTP and stdio, not browser interaction with the Web UI.
-
 ## End-to-end, integration and golden evidence

 The optional `verify:qwen-client`, `verify:pi-client`, and `verify:hermes-client`
@@ -486,7 +462,7 @@ existing static JavaScript analysis through CLI and stdio MCP, including
 manifest readback, competing query variants, and resolved relative imports.
 It uses an installed browser and accepts an optional installed REA entrypoint.
 The complete `verify:browser` lane also exercises passive script export through
-both public adapters. See [website script export](../guides/web/website-script-export.md).
+both public adapters. See [website script export](website-script-export.md).

 `verify:browser:modules` compares CLI and stdio MCP traces against an independent
 real Chromium module-loading fixture: import-map scopes, package prefixes,
@@ -494,7 +470,7 @@ null/backtracking rejection, query/fragment identities, repeated module instance
 lazy and computed unknowns, exact source/map identities and no implicit refetch.
 Set `REA_BROWSER_EXECUTABLE`; the optional script argument selects an installed
 package entrypoint. The complete `verify:browser` lane and existing conditional
-Chrome CI include this verifier. See [module relationships](../guides/web/website-module-trace.md).
+Chrome CI include this verifier. See [module relationships](website-module-trace.md).

 ## Agent evaluation and conformance records

@@ -3,7 +3,7 @@
 This guide explains the runtime settings design for maintainers and developers:
 who owns each value, when an update takes effect, how providers enforce it, and
 how to extend the system. The public tool contract is in
-[MCP contracts](../reference/mcp-contracts.md#editable-analysis-settings); recorded runtime
+[MCP contracts](../mcp-contracts.md#editable-analysis-settings); recorded runtime
 checks and their limitations are in the
 [verification report](../verification/runtime-analysis-settings.md).

@@ -121,22 +121,9 @@ launch environment affects the next REA process.
 is the byte-budget shape: a decimal safe integer with a 10 MiB floor
 (`MINIMUM_RESPONSE_BYTES`), the same shared schema, and no silent fallback. A
 change needs a REA restart and a matching client receive buffer. It does not
-raise REA's reserved string limit or Node's string ceiling. Like the regex
-deadline, it is in `SELECTED_REGISTRATION_SETTINGS`, so setup forwards an
-explicit selection into the client registration.
-
-Windows ChangeTime admission waits out a fresh timestamp before recording a
-baseline. `REA_WINDOWS_CHANGE_TIME_DRIFT_MS` (default 2000 ms, floor 1 ms,
-maximum 60000 ms), `REA_WINDOWS_CHANGE_TIME_SETTLE_POLL_MS` (default 25 ms,
-floor 1 ms, maximum 1000 ms), and `REA_WINDOWS_CHANGE_TIME_SETTLE_MAX_POLLS`
-(default 40, floor 1, maximum 1000) are launch settings. Unset keeps those
-defaults. An invalid value is a configuration error: it names the setting, the
-rejected value, source `setting`, the default, the floor, and the maximum, and
-says to set a positive decimal integer in the environment that starts REA and
-then restart REA. There is no runtime override. Setup forwards an explicit
-selection. When the poll budget runs out, admission keeps the last observation
-instead of failing the readable file. Raising a setting only changes how long
-that wait can last. It does not change Windows ChangeTime itself.
+raise REA's reserved string limit or Node's string ceiling. The setup
+allowlist does not copy this setting. A new headroom setting should, following
+the regex deadline.

 A per-call budget can have a runtime default without having an environment
 setting. JavaScript `max_heap_mb`
@@ -399,7 +386,7 @@ application points, and resulting behavior. Check that adapters deliver the
 canonical recovery guidance, with independent assertions for its underlying
 facts. Avoid freezing prose or deriving all expected values from the same
 registry used by the implementation; either can hide the wrong failure.
-See [test design](../development/testing.md#test-design-and-pruning) for the assertion policy.
+See [test design](../testing.md#test-design-and-pruning) for the assertion policy.

 Runtime checks cover atomic validation, stale writes, reset, runtime isolation,
 accepted-operation snapshots, and explicit argument precedence. Public MCP
@@ -1,379 +0,0 @@
-# Desktop application capture
-
-`rea capture-desktop-application` launches an installed Linux desktop
-application, watches it while a person or a driver uses it, and records what
-it is, which windows it opened and how the files under the home directory
-changed. The result is the starting point for turning the application into an
-agent environment: the inventory says how to install and launch it, the windows
-say how to recognise it, and the checkpoints hold the state it read and wrote.
-
-The application runs with the current user's permissions, in the current
-desktop session, against the user's real files. This is not a sandbox. The
-capture folder keeps copies of real files from the home directory, so treat it
-as private data and keep it local.
-
-## Host support
-
-Capture runs on Linux with an X11 display: `DISPLAY` must be set, and `xprop`
-(from `x11-utils`) must be installed, or `REA_XPROP_COMMAND` must name it.
-The window manager must support the EWMH client list (`_NET_CLIENT_LIST`,
-listed in `_NET_SUPPORTED`), as xfwm4, Mutter, KWin and Openbox do; without it
-the capture is refused, because no window could be seen. A supported list that
-is unset, as xfwm4 leaves it while no window is open, means no windows. Applications that run under XWayland are visible;
-native Wayland windows are not. Other hosts are refused before anything is
-launched.
-
-## Capture an application
-
-Name the application by its desktop entry id, the entry's absolute path, or an
-executable:
-
-```sh
-rea capture-desktop-application --desktop-entry org.xfce.mousepad --output ./mousepad-capture
-rea capture-desktop-application --executable gnucash --argument /home/ada/books.gnucash --output ./gnucash-capture
-```
-
-Desktop entries are looked up in `$XDG_DATA_HOME/applications` and then each
-`$XDG_DATA_DIRS` directory; an entry installed as a symbolic link, as flatpak
-and Nix do, is followed to its file. The entry's `Exec` line is expanded with no files;
-`--argument` values are appended in its place, and the application runs in the
-entry's `Path` or the home directory. When the line starts with
-`env NAME=value`, the program is found on the `PATH` those assignments set,
-with an empty or relative entry read from the folder the application runs
-in, and their XDG folders name the state directories. Otherwise the program is
-looked up on the host's `PATH` in the order the launch searches it, and one
-found only through a relative or empty entry is refused, since the exported
-computer would not have that entry. An `--executable` runs from
-the current directory, as it would from a shell, and a relative path to it is
-resolved there.
-
-Before writing anything the command refuses to start if a window of the
-application is already open, or if the window list cannot be read. A launch
-beside a running instance can hand off to it, and that instance's unsaved
-state would be missing from the baseline. It then records the starting state,
-launches the application in its own process group with a run token in its
-environment, and reads commands from stdin, one per line. The application gets
-REA's environment without the `AGENTENV_*` variables an agent environment sets,
-such as its control token: an app the exported computer launches never has
-them, and an app captured inside a computer must not hold a credential to it.
-
-| Line                                        | Effect                                                      |
-| ------------------------------------------- | ----------------------------------------------------------- |
-| empty, `checkpoint`, or `checkpoint <name>` | Record the current state as a checkpoint                    |
-| any other text except `stop`                | Record a checkpoint named by that text                      |
-| `stop`, or the end of stdin                 | Record a final checkpoint, close the application and finish |
-
-An unnamed checkpoint is named `checkpoint-<ms>` after its time in the
-session. A name that repeats an earlier checkpoint, or is one of the capture's
-own names (`baseline`, `stop`, `time-limit`, `exit`), is refused with a
-progress line on stderr; no checkpoint is taken and the session continues.
-
-Name the checkpoints a later step reads by what they mark. The
-[export](desktop-application-export.md) seeds the bundle from the baseline
-unless `--seed-checkpoint` names another, and a
-[task](desktop-application-tasks.md) is checked against the last checkpoint
-unless `--end-checkpoint` names another. So one capture can build a seed and
-then the change: launch the app, create and save the document, send
-`checkpoint seed`, make the edit and save it, send `checkpoint end`, then
-`stop`.
-
-The session also finishes when the launched process has exited and the
-application's processes and windows are all gone in two consecutive samples,
-or when `--max-duration-seconds` passes. Before deciding the processes are
-gone, the capture looks for any process still carrying the run token, so a
-worker whose launcher exited before it was sampled keeps the session open. A
-sample whose window list could not be read is not taken as an empty one; the
-limitations say how many there were. One queued line is handled between
-samples, and reading stdin pauses while 16 lines wait.
-
-Progress lines on stderr are JSON, `{"rea_progress": {"phase":
-"desktop_capture", "message": ...}}`. Those a driver waits on also carry an
-`event`: `{"kind": "window_open"}` once the window opens; `{"kind":
-"checkpoint", "name", "trigger", "at_ms", "entries", "changes",
-"retained_files", "retained_bytes"}` once a checkpoint has been taken, the
-baseline, `stop` and `exit` included, with the paths walked, the paths
-changed since the checkpoint before and the files retained; and `{"kind":
-"checkpoint_refused", "name", "reason"}` for a requested name it refused. A
-driver that sends `checkpoint <name>` waits for the event naming it rather
-than for a fixed time.
-
-When the session ends the capture sends SIGTERM to the launched process, its
-process group and every process that carries the run token, waits up to five
-seconds for them to exit, and then removes every process that still carries
-the token, whether or not it stayed in the process group. If that cleanup
-cannot be verified after a second attempt, the capture is still written, and
-the command then fails, naming the run token and process group that may
-remain. Interrupting the command (Ctrl-C) ends the session the same way
-without a further checkpoint; the capture is still written with end reason
-`cancelled`, and the command exits with status 130. Interrupted before the
-application is launched, the command writes no capture and removes the
-content it had retained.
-
-If the capture fails for any other reason before `capture.json` is written,
-the application is closed the same way and the content already retained is
-removed from the capture folder. The error names any process or file that
-could not be removed.
-
-A person types these lines in the terminal. An agent can drive the
-application with a tool such as `xdotool` and write the lines to a FIFO that
-it passes as stdin. Because the end of stdin stops the session, the driver
-must keep the FIFO open for writing between checkpoints, for example with
-`exec 3>capture.fifo` in a shell, rather than open and close it for each
-line.
-
-| Option                   | Default | Meaning                                                                                   |
-| ------------------------ | ------- | ----------------------------------------------------------------------------------------- |
-| `--state-path`           | none    | File or directory whose starting content is retained too (repeatable)                     |
-| `--exclude`              | none    | Path left out of every checkpoint walk (repeatable); the output folder is always left out |
-| `--max-duration-seconds` | 3600    | Stop the session after this long                                                          |
-| `--max-entries`          | 250,000 | Paths recorded per checkpoint walk, its roots included                                    |
-| `--max-file-bytes`       | 64 MiB  | Largest file whose content is retained                                                    |
-| `--max-content-bytes`    | 1 GiB   | Total retained content                                                                    |
-| `--package-file`         | none    | The `.deb` file the application was installed from; its facts are recorded, not the file  |
-
-`--state-path`, `--exclude` and `--output` refuse an empty value, which
-would otherwise name the current directory.
-
-## The capture folder
-
-The output folder must be new, or empty and owned by the current user; the
-command makes it private (mode 0700). It holds:
-
- `capture.json`: the Evidence record, also printed on stdout.
- `content/<sha256>`: the bytes of each retained file, stored once per
-  distinct content.
-
-The Evidence operation is `capture_desktop_application` and its predicate type
-is `rea.desktop-application-capture`. Its `host` names the platform,
-architecture, display and home directory, and the host's name (`hostname`)
-and the user's (`user`), which captured state can hold, as in a mail
-template's `ada@e81232be457d`; the export removes them from the bundle. A
-capture written before they were recorded has neither, and one is left out
-when the system cannot say, as for a user with no passwd entry. The rest of
-the result has four parts.
-
-**Application.** The desktop entry (id, path, name, `Exec`, icon,
-`StartupWMClass`, categories, MIME types), the launch command and working
-directory, the executable as found on `PATH` and after resolving links, and the
-package that installed it. A Debian package records its name, version,
-architecture and the apt sources that list the installed version, with the
-origin (`o=`) apt reports for each source in `source_origins`, such as `Ubuntu`
-for the Ubuntu archive and its mirrors or `LP-PPA-<name>` for a PPA; an empty
-source list means the version came from a local `.deb` or the package lists
-are missing, which `package_lists_present` tells apart. apt's lists folder,
-and the trusted keys below, are where `apt-config` resolves
-`Dir::State::Lists`, `Dir::Etc::TrustedParts` and `Dir::Etc::Trusted` under
-`Dir`, so an `APT_CONFIG` file that moves them is followed: on a computer
-without lists, an ordinary user can run `apt-get update` with an `APT_CONFIG`
-naming writable `Dir::State::Lists` and `Dir::Cache` folders and capture with
-the same `APT_CONFIG`. Without `apt-config`, or when it fails, they are
-`/var/lib/apt/lists`, `/etc/apt/trusted.gpg.d` and `/etc/apt/trusted.gpg`.
-
-The Debian package is the one `dpkg-query -S` names as the owner of the
-desktop entry the capture launched, or else of the executable, since the
-entry's package is what installs the application: LibreOffice Writer's entry
-belongs to `libreoffice-writer`, while the `/usr/bin/libreoffice` it runs
-belongs to `libreoffice-common`, which does not bring Writer with it. When the
-two differ, `executable_package` names the executable's package, which the
-export installs beside the entry's, since the entry's package need not depend
-on it (`vim-common` owns Vim's entry but does not depend on `vim`).
-`executable_package_reason` says why the computer could not install it by
-name, by the rule for library packages below: neither the Ubuntu 24.04 archive
-nor a vendor repository the export declares offers it, or `apt-cache policy`
-did not say. When a package owns the entry but none owns its program, such as
-a `~/.local/bin/<name>` found first on `PATH`, the entry's package is recorded
-without `executable_package`, and `executable_package_reason` says no package
-owns the program, so the export refuses rather than install a package that
-does not bring it. A program link that dpkg does not own counts as owned when
-dpkg owns the file it resolves to, as an alternatives link does. An
-`--executable` launch, or an entry no package owns, such as
-one in `~/.local/share/applications`, records the executable's package. When
-`dpkg-query` does not finish or exits with an error for the executable or the
-entry, the package is `unknown` and the limitations say which path, since a
-failed lookup is not proof that no package owns it. The sources, vendor
-repositories and `--package-file` match below are the recorded package's; the
-library walk still reads the executable.
-
-Each source whose origin is not `Ubuntu` is also recorded in
-`apt_repositories`. `apt-get indextargets` names the sources file entry apt
-read it from and its release, so flat repositories match too, whether their
-suite is `./` (Typora's `deb https://downloads.typora.io/linux ./`) or `/`
-(pkgs.k8s.io's). The record holds that entry (`sources_file`, `uri`, `suite`,
-`components`, none for a flat repository, and `architectures`, the entry's
-`arch=` or `Architectures:` restriction, empty when it has none), `release`,
-the release's Suite (apt's `a=`) or else its Codename, and the key that signs
-it. A user name or password in an entry's URI (`https://user:password@host/…`)
-is never recorded: REA removes it from every URI it reads, in the sources file
-and in `apt-get indextargets` and `apt-cache policy` output alike, so entries
-match whether or not apt prints it, and sets `uri_credentials_removed` on a repository whose URI held
-one (a capture written before this was recorded omits the field). The key is
-found by verification, not by name: the candidates are the
-entry's `signed-by` keyrings, or else every `.gpg` and `.asc` key in apt's trusted
-parts folder and its trusted keyring, and each is checked with
-`gpgv` against the release's `InRelease` (or `Release` with `Release.gpg`)
-beside its index in apt's lists folder. A deb822 entry whose `Signed-By` field
-holds the armored key itself, as `add-apt-repository ppa:<owner>/<name>`
-writes it on Ubuntu 24.04, has that key as its only candidate, as apt trusts
-no other for it: REA reads the field's continuation lines as deb822 writes
-them, a `.` line standing for an empty one, from the key block's `BEGIN` line
-to its last `END` line, and records the key's path as the entry's sources
-file. A key counts when gpgv reports a valid signature by it and no bad,
-expired, revoked or unverifiable signature by it, whatever gpgv's exit status:
-a release also signed by a key the host lacks makes gpgv fail. Each candidate
-is copied, an armored key decoded to a binary keyring, into a private
-temporary folder that is removed afterwards; a folder REA cannot remove
-fails the capture with the folder as its cleanup resource. The key that
-verifies is recorded in `signing_key` with its path,
-SHA-256, format (`binary` or `armored`) and primary fingerprint, and its bytes
-are retained under `content/`. A key file holding one key is retained as it
-is; from one holding several, such as a legacy `/etc/apt/trusted.gpg`, only
-the transferable key with the verifying fingerprint is retained, in binary, so
-the bundle trusts no other key. When no candidate verifies, `gpgv` is
-missing, apt holds no signed release, no sources entry matches, the key the
-entry's `Signed-By` holds does not verify the release, or the key is larger
-than `--max-file-bytes` or the content budget, `signing_key` is null and
-`signing_key_reason` says why. Ubuntu Pro's ESM repositories (origins such as
-`UbuntuESMApps`, host `esm.ubuntu.com`) are not checked: apt reaches them only
-with the host's Ubuntu Pro credentials, which a computer does not have.
-
-Unless the installed version comes from the Ubuntu 24.04 archive, so for a
-vendor repository's package and for a local install that no apt source lists,
-`library_packages` lists the packages that own the shared libraries the
-executable loads at start; the walk runs beside the repository check, and not
-at all for an archive package, whose export does not use it. REA reads
-DT_NEEDED from the resolved executable and from each library it finds, and
-looks each soname up as ld.so does: in the RPATH of the needing image and of
-each image up its chain of loaders to the executable when the needing image
-has no RUNPATH, then in its RUNPATH (with `$ORIGIN` expanded and paths
-normalized), and then in the `ldconfig -p` cache entries for the executable's
-machine. It asks `dpkg-query -S` for each library's package. Libraries in the
-executable's own folder belong to the application: they are walked but not
-listed, and neither is the application's own package. One batched
-`apt-cache policy` then keeps only the packages the Ubuntu 24.04 archive or a
-recorded vendor repository with a verified key offers, in any component its
-sources entry lists, since the export declares them all; the rest, such as
-packages from a PPA or a local `.deb`, are listed in
-`uninstallable_library_packages`. The same query checks `executable_package`.
-Each recorded repository's `supplies` lists the kept packages, and the
-executable's package, that the archive does not offer and its package files
-list, so the export can leave out those only a repository it does not declare
-supplies, such as one whose key the content budget later dropped. Sonames
-found nowhere are listed in
-`missing_libraries`, and libraries no package owns in `unpackaged_libraries`.
-`library_packages_reason` says why the lists are incomplete: the executable is
-not an ELF image (a launcher script, for example), `ldconfig`, `dpkg-query` or
-`apt-cache` is missing, a library could not be read or names more than 512
-libraries, or the walk stopped after 512 libraries.
-
-A sources file, key or library whose handle REA cannot close fails the capture
-with the file as its cleanup resource. When the repository check and the
-library walk both fail, the capture reports both failures and every folder or
-file either could not release.
-
-An application installed from a `.deb` file you downloaded, such as VariCAD
-from varicad.com, has no apt source a computer could install it from. Name
-that file with `--package-file` so the export can have the computer download
-it instead. REA reads the file's control fields with
-`dpkg-deb --field FILE Package Version Architecture Depends Pre-Depends`, and
-when its Package, Version and Architecture are the installed package's, it
-reads the file once more for its SHA-256 and size and records `package_file`:
-the file's `name` without its folder, `sha256`, `size`, `package`, `version`,
-`architecture`, and the `depends` and `pre_depends` entries as the file
-declares them. Otherwise `package_file_reason` says why, for example that
-`dpkg-deb` is not installed, that the file holds another version than the
-installed one, or that the file changed between the two reads (its device,
-inode, size and times are compared), since its fields and its hash could then
-describe different files. The capture never copies the file: it is the vendor's, and only
-these facts are kept.
-
-Snaps, flatpaks and
-AppImages are recognised from their paths, and flatpaks also from a
-`flatpak run` launch, whose application id is the first operand after
-flatpak's options and their values. Electron applications are marked by
-the fuse sentinel in their binary or a `resources/app.asar` beside it. State
-directories are the XDG config, data, state and cache folders and the
-dot-folder named after the package, the executable, the desktop entry's full
-id and its last part, and the entry's name, with whether each existed at the
-start. A folder in those places whose name is one of these in another letter
-case joins them, such as GIMP's `~/.config/GIMP` for the `gimp` package; only
-the whole name is compared, so `~/.config/GIMPshop` does not. Dotfiles in the
-home named after the application (`.<name>rc`, or
-`.<name>` followed by `-`, `.` or `_`, for a name of three or more characters)
-that exist at the start join them, since an application may only read such a
-file during the capture. A `flatpak run` launch is named after its application
-id rather than the `flatpak` launcher, and adds `~/.var/app/<id>`.
-
-**Session.** When it started, how long it ran and why it ended; the launched
-process's exit status; every process seen in the application's tree; every
-client window with its class pair, titles, owner pid and type, marked when it
-belongs to the application; when the first application window appeared; the
-most common class pair of the application's windows, for matching its window
-later; files the application's processes held open under the walked roots; the first
-8 KiB of the launched process's stderr; and whether cleanup was verified. Each
-process records whether the capture started it: the launched process, a
-process carrying the capture's run token, or a descendant of one, even when
-its environment cannot be read, as for a zombie or a sandboxed renderer.
-Processes are told apart by their start time, so a pid reused by another
-process is not counted as the application's.
-
-A window belongs to the application when its owner pid is one of the
-application's live processes or its class matches the desktop entry's
-`StartupWMClass`, the executable's name, the entry's full id or its last part,
-or a flatpak's application id. A flatpak's windows report pids from its
-sandbox, so they are matched by class only.
-Ownership is checked again at every sample, because a window can appear before
-the process that owns it is found. A matching window's pid joins the
-application's processes, so a launch handed to a process the capture did not
-start, such as a D-Bus activated service, is still followed. That process does
-not carry the run token, so the capture never signals it and leaves it
-running.
-
-**State.** The walked roots (the home directory plus any content root
-outside it), the content roots (state directories, `--state-path` values and
-absolute `--argument` values, except `/` or a directory that contains the home
-directory, which are named in the limitations instead; a selected path that is
-not a directory brings the `-wal` and `-journal` paths beside it, so a database
-selected on its own is captured with its logs), the state directories
-as walked (their physical spelling, which differs from the inventory's when one
-is a symlink), the paths every walk left out (the output folder and
-`--exclude` values), and the checkpoints in order: `baseline` before
-launch, each requested checkpoint, `stop` or `time-limit`, and `exit` after the
-application has gone. Each checkpoint records how many paths its walk saw,
-whether it was truncated, how many paths it could not read or directories on
-another device it did not enter (`unchecked_paths`), which paths were created, modified, deleted or
-changed type since the previous checkpoint, and which files it retained. A
-path counts as created or deleted only where the walk listed its nearest
-existing directory completely; differences under a directory that could not be
-listed, or that a truncated walk did not reach, are counted as unconfirmed
-instead. A walk does not enter a directory on another filesystem than its
-root, such as an NFS, sshfs or other FUSE mount under the home directory; the
-limitations list each such mount point. The
-baseline retains every file under the content roots; later checkpoints retain
-every changed file. A change records the file's type, size, mode,
-modification time and, when known, the SHA-256 of its content before and
-after, plus whether it lies in a state directory and whether the application
-held it open. A file is retained only if it is still the version the walk
-recorded and does not change while it is read. A file larger than the
-remaining content budget is not read, unless stored content of the same size
-could make it a duplicate. Files that could not be
-retained are listed with the reason: too large, over the content budget,
-changed since the walk, changed during the read, or unreadable.
-Directories the application held files open in, but whose starting content was
-not retained, are listed so a second capture can pass them with
-`--state-path`.
-
-**Limitations.** What the capture could not establish, such as a truncated
-walk or a missing window.
-
-## What the capture does not establish
-
-Changes are found by comparing walks, using each path's size, modification
-time, inode and mode, so a change undone between two checkpoints is not seen
-and a rewrite that keeps all four is missed. A change is not attributed to the
-process that made it: other desktop services write under the home directory
-too, such as the dconf database, the window manager's settings and GTK's
-recently used list. The markers for state directories and open files are
-evidence for attribution, not proof.
-
-Clicks and keystrokes are not recorded. Window titles are sampled every half
-second, so short-lived titles can be missed.
@@ -1,342 +0,0 @@
-# Desktop application export
-
-`rea export-desktop-application <capture-folder> <directory>` turns a folder
-written by [desktop application capture](desktop-application-capture.md) into an
-agentenv bundle holding one computer app environment: the real application,
-installed from the distribution archive, its vendor's apt repository or the
-`.deb` file it was installed from on the `ubuntu-24.04` computer base, launched
-at boot, seeded with the user's state and serving that state through agentenv's
-data operations.
-
-```sh
-rea export-desktop-application ./mousepad-capture ./mousepad-bundle
-agent-env run ./mousepad-bundle --dry-run
-```
-
-The export reads the capture and its [state view](desktop-application-state.md);
-it does not run the application. `--name` sets the environment name; otherwise
-it comes from the desktop entry id or the program, with an `app-` prefix when
-that name would not be a portable bundle name (for example all digits). The
-output directory must be new or empty. `--task` adds a task an agent wrote for
-the capture, once REA has validated it against the capture; see
-[desktop application tasks](desktop-application-tasks.md). `--package-url`
-says where the computer downloads the package of an application installed from
-a `.deb` file; see [Applications from a .deb file](#applications-from-a-deb-file).
-`--seed-checkpoint` names the checkpoint whose state seeds the bundle, the
-baseline by default, and `--end-checkpoint` the one a task must pass on, the
-capture's last by default; see [The seed checkpoint](#the-seed-checkpoint).
-
-The command returns Evidence with operation `export_desktop_application` and
-predicate type `rea.desktop-application-export`, listing the environment name,
-the seed and end `checkpoints`, owned paths, seed files, the seeds it
-rewrote to remove the capture host's name and user (`scrubbed_files`), the
-bundle files that still hold them (`unscrubbed_files`), and written files,
-the last three by their path in the bundle. A failed export, cancellation
-included, removes the bundle it had not yet published, so no partial copy of the
-user's data remains. If the bundle was published but its output handles could
-not be closed, the command reports a cleanup error that carries the export
-Evidence; the bundle itself is complete.
-
-## The bundle
-
-| Path                             | Contents                                                                                           |
-| -------------------------------- | -------------------------------------------------------------------------------------------------- |
-| `envs/<name>/env.toml`           | `type = "computer_app"`, the module and class, `computer = "ubuntu-24.04"`, `driver = "reference"` |
-| `envs/<name>/<file>.py`          | The `ComputerAppEnvironment` class                                                                 |
-| `envs/<name>/SKILL.md`           | What the app is, its window class and where its files live                                         |
-| `envs/<name>/seed/`              | The application's files at the seed checkpoint, by home-relative path                              |
-| `envs/<name>/apt-keys/`          | The signing key of each vendor apt repository the app installs from                                |
-| `envs/<name>/install-package.sh` | With `--package-url`: the run script that installs the downloaded package with dpkg                |
-| `tasks/smoke.json`               | A task that deploys the app                                                                        |
-| `tasks/<task>.json`              | With `--task`: the agent's task, its verifier in `artifacts/` and the eval in `evals/`             |
-| `README.md`                      | What was exported, from which capture, and what to keep in mind                                    |
-
-The class file is `<name>_app.py` with hyphens as underscores, for example
-`mousepad_app.py`: agentenv imports it under its stem, so a plain `<name>.py`
-could shadow a standard library module such as `calendar`. A class name that
-would collide with a name the module imports or defines, such as `Path`, takes
-an `App` suffix.
-
-The class declares:
-
- `Packages(apt=[...])` with the package the capture found. A vendor package
-  is named `<package>/<release>`, its repository's release (the Suite apt
-  reports as `a=`, or else its Codename), so apt takes it from that repository
-  even when the Ubuntu archive offers a higher version or epoch, as noble's
-  transitional `firefox` does over packages.mozilla.org's; it is named alone
-  when the release names neither, or when the capture was written before
-  releases were recorded. Its library packages follow, so a package that
-  leaves out dependencies on the libraries it loads, as Typora's Electron
-  package does, still starts; library packages the capture found neither the
-  Ubuntu 24.04 archive nor a declared repository offers are left out, with a
-  limitation, and so are those only repositories the export leaves out supply
-  (a repository's `supplies`), such as one whose key the capture could not
-  retain. An archive package's declared dependencies are trusted as they
-  are. When the desktop entry's package is not the one that owns the program
-  it runs, as `vim-common`'s entry runs `vim`'s program, the program's package
-  (`executable_package`) follows the app's by name, since the entry's package
-  need not depend on it; a capture that found no archive or declared
-  repository offering it records why, and the export refuses it with that
-  reason, as it does when only repositories it leaves out supply it, or when
-  no package owns the program at all (`executable_package_reason` without
-  `executable_package`). The package must come from the Ubuntu 24.04 archive
-  or a mirror of it,
-  or from a vendor apt repository whose signing key the capture verified and
-  retained. A source counts as the archive when apt reports its origin as
-  `Ubuntu` for a noble suite; a capture made before origins were recorded
-  counts only Canonical's own archive hosts.
- For a vendor repository, `sources=[AptSource(apt=..., suite=...,
-  components=[...], key="apt-keys/<name>.gpg")]`, with the retained key copied
-  to that path (`.asc` when it is armored, which agentenv tells by its
-  content). A PPA added with `add-apt-repository`, whose sources entry holds its
-  key in `Signed-By`, exports that key as `apt-keys/<name>.asc`. apt takes one
-  key per URI and suite, so sources that share them, such as one repository
-  listed for two architectures, are declared once, with their components
-  merged; one with a different key is left out. A repository
-  whose key the capture did not verify, an Ubuntu Pro (ESM) repository, one
-  whose sources entry's URI held a user name or password (which the capture
-  did not record and the export never writes; the reason names neither them
-  nor the URI), one not reached over http or https, or one whose `arch=`
-  restriction leaves out the capture host's architecture is refused with its
-  reason (a capture
-  written before restrictions were recorded counts as unrestricted); when
-  another usable repository lists the same version it is left out instead,
-  with a limitation. The export also refuses snaps, flatpaks, AppImages, and a
-  package no recorded repository lists unless it was installed from a `.deb`
-  file the capture recorded and `--package-url` is given, since the computer
-  could not install them by name, and a capture written before credentials
-  were removed whose repository URI still holds them, since it counted that
-  repository's libraries as installable; capture it again.
- `@computer_app(supports=...)` with both `amd64` and `arm64` for an archive
-  package, which the archive serves for both, and only the capture host's
-  architecture for a vendor package, since its repository may serve no other.
-  A vendor package captured on any other architecture is refused. A package
-  installed from its `.deb` file supports only that file's architecture.
- A launch at boot with the captured command, ready when a window of the
-  captured class appears and one of them is listed in the taskbar and is not
-  typed as a splash: a splash screen or a dialog of the class skips the
-  taskbar or says it is a splash, and an app whose splash shows first would
-  otherwise count as ready before its own window opens. Arguments that are the captured home or under it, and
-  `<option>=<path>` values under it, are respelled under the computer user's
-  `$HOME`. agentenv starts the app in its own folder, where an open or save
-  dialog would show the framework's files, so the command first changes to the
-  captured working directory (`"$HOME"` when that was the home, as for a
-  desktop entry without `Path`), which a relative argument or program path
-  such as `./app` also needs, and still starts if that folder is missing. The
-  export refuses a capture that saw no application window.
- For an Electron application (the capture found its fuse sentinel or a
-  `resources/app.asar`), `--no-sandbox` right after the program unless the
-  command already has it: Chromium's sandbox needs user namespaces the
-  computer's container does not grant, and Electron exits without them. The
-  README and the result's limitations say the sandbox is off.
- `paths`: the state directories holding the application's state files and the
-  folders holding its documents, nested folders collapsed. A folder beside a
-  state directory whose name differs from it only in letter case is owned
-  whole in the files' spelling, so a `~/.config/GIMP` profile GIMP created
-  during the capture beside the candidate `~/.config/gimp` is owned as
-  `.config/GIMP`, not as the folder of its first file. The home itself and
-  the shared `.config`, `.local`, `.local/share`, `.local/state` and `.cache`
-  folders are never owned whole: a file directly in one is owned as itself.
-  Files the capture recorded under a symlinked state directory's physical
-  spelling are mapped back to the innermost such directory's home spelling,
-  unless that spelling is outside the captured home, as when the home itself is
-  a symbolic link. When two files map to one home path, the export uses the one
-  present before the capture, else the first by path, and a limitation names
-  the other.
- Data hooks, because declaring any hook switches off agentenv's default data
-  plane: the class seeds the home once per boot and keeps it as the initial
-  state with `keep_initial`, `data/add` and `data/reset` call agentenv's `add`
-  and `reset`, and `data/get` returns the files under `paths` plus a data part
-  with a typed JSON view of each, read in a worker thread. An application with
-  no observed state declares no paths and no hooks.
-
-A file under the owned paths whose bytes at the seed the capture did not
-retain is not seeded: one in the state view without retained content at that
-checkpoint, or one the capture omitted (for example too large or past the
-content budget). The result lists them in `unseeded_files` and the README
-names them. When the application held files open in folders whose starting
-content the capture did not retain, a limitation names those folders. The
-desktop Trash, `~/.local/share/Trash`, is never the application's, so a file
-the user moved there is neither owned nor seeded, even when a window title
-names it; a limitation lists the files the Trash held at the seed.
-
-The application's dconf keys at the seed, if any, are written once when the
-app first starts, also for an application that owns no files, and the class adds
-`dconf-cli` to its apt packages for that. The server starts before the
-desktop's D-Bus session, so the class does not use `dconf load`: it dumps any
-existing user database through a `file-db:` profile, then runs `dconf compile`
-on that dump and the captured keys, in that name order so the captured keys
-win, and replaces `~/.config/dconf/user`. If that fails, the server prints a
-one-line warning and the app starts without the captured keys. `data/reset` does
-not restore them.
-
-## The seed checkpoint
-
-By default the seed is the state before the capture, its `baseline`, and a
-task's end state is the capture's last checkpoint. `--seed-checkpoint` and
-`--end-checkpoint` name others, so one capture can make a seed and then a
-change: the user creates and saves a document and takes `checkpoint seed`,
-then edits and saves it and takes `checkpoint end`. Exported with
-`--seed-checkpoint seed --end-checkpoint end`, the bundle seeds the document
-as it was saved at `seed`, owned paths, dconf keys and unseeded files
-included, and a task must fail on that seed and pass on the state at `end`.
-A file's state at a checkpoint is its last version recorded at or before it.
-The export refuses a name the capture does not hold exactly once, and an end
-checkpoint taken before the seed checkpoint; `inspect-desktop-application-state`
-lists the names in `capture.checkpoints`.
-
-## Host name and user
-
-A seed can hold the capture host's name and the user's: Geany saved its mail
-template as `pref_template_mail=ada@e81232be457d`, the user `ada` on a
-container named `e81232be457d`, and many files hold the home path
-`/home/ada`. The capture records `host.hostname` and `host.user`, and the
-export removes them from what the bundle ships:
-
- In seeded text files (text, JSON, key files and XML in the state view), in
-  UTF-16 files that start with a byte-order mark (keeping the mark, byte order
-  and a following U+FEFF content character), and in the dconf keys,
-  `user@host` becomes `user@localhost`, the
-  host name standing alone becomes `localhost`, and the captured home becomes
-  `/home/user` wherever it is followed by `/`, the end of the text, or a
-  character that cannot continue a file name. The host name counts only as a
-  whole name: not inside a longer word, before a `-`, or as a label of a
-  domain such as `e81232be457d.local`, so a host named `ubuntu` leaves
-  `ports.ubuntu.com/ubuntu-ports` alone. A host named `localhost` is left
-  alone, but its `user@localhost` still takes the computer's user. The user
-  name alone is never replaced, since a short one such as `ada` or `user` is
-  also ordinary text. A rewritten seed is written with its own SHA-256, and
-  `scrubbed_files` and the README list it.
- JSON and XML keep their syntax. In JSON only string values change, each
-  read as its decoded value, so `\u0065` escapes cannot hide the host, and is
-  written back as JSON only when it changed; numbers and `true`, `false` and
-  `null` stay as they are even for a host named `true`. Member names are never
-  rewritten, since `{"ubuntu": 1, "localhost": 2}` on a host named `ubuntu`
-  would get two `localhost` keys and lose a setting; a file whose names hold
-  the host is listed in `unscrubbed_files` instead. In XML only character
-  data, attribute values, comments and CDATA change, character references
-  decoded the same way; element and attribute names and processing
-  instructions stay. A UTF-16 file is scrubbed by the format its text would
-  have in UTF-8, so JSON or XML in UTF-16 follows these rules too.
- In the dconf keys only GVariant strings change, each read as its decoded
-  value and written back in its own quotes only when it changed. Group names,
-  keys, dictionary keys, bytestrings and everything outside quotes stay, so a
-  host named `true` leaves `wrap=true` alone. A value whose string does not
-  parse, or that holds an object path or signature, ships as captured.
- `SEED_HOME` in the class is `/home/user`, the home the seed spells, which
-  the class respells to the computer's own home when it seeds the home at
-  boot, as it did the captured home before. The replacements read as the
-  computer's own: its user is `user`, with its home in `/home/user`, and
-  `localhost` is the name every host has for itself.
- Binary files, SQLite databases among them, and text files over 256 MiB are
-  copied as captured. Then every file the bundle ships, the class module with
-  its dconf keys and the README included, is searched by a looser rule than
-  the replacement's: the host name and `user@host` anywhere, as in
-  `e81232be457d.local` or a seed named `e81232be457d-notes.txt`, and the
-  captured home as a whole path, in its path and its content, JSON and dconf
-  strings and XML references decoded and the replacements themselves set
-  aside. Each one found is listed in `unscrubbed_files`, and in the README
-  unless it is the README, to check before sharing the bundle. Bytes that are not text are
-  searched as they are, so a binary file that holds the host in another
-  encoding is not listed.
- A task check whose values name `user@host` or the host name anywhere, by
-  that rule, is refused, as one naming the captured home is: the bundle does
-  not hold them. Its field names, kind and id are not values, so a host named
-  `file` or `kind` refuses no check. A task's checks must fail on the seed as
-  the bundle ships it, scrubbed, so a check the scrub itself satisfies, such
-  as a mail setting the user changed from `ada@e81232be457d` to
-  `user@localhost`, does not count as failing there.
-
-A capture written before the host's name and user were recorded has only its
-home removed, with a limitation saying so; capture again to remove the rest.
-
-## Applications from a .deb file
-
-A closed-source application you installed from a `.deb` file you downloaded,
-such as VariCAD from varicad.com, is not in any apt repository the computer can
-use. Capture it with `--package-file` naming that file (see
-[desktop application capture](desktop-application-capture.md)), then pass
-`--package-url` to the export with an `http://` or `https://` URL the computer
-can download that same file from:
-
-```sh
-rea capture-desktop-application --executable varicad --package-file ~/Downloads/varicad2026-en_2.03_amd64.deb --output ./varicad-capture
-rea export-desktop-application ./varicad-capture ./varicad-bundle --package-url https://files.example.com/varicad2026-en_2.03_amd64.deb
-```
-
-The class then declares, beside `Packages`:
-
- `downloads=[Download(url=..., sha256=..., to="vendor/<file>", arch=...)]`
-  with the captured file's SHA-256. agentenv downloads the URL once, when the
-  bundle is put, and refuses the file unless its SHA-256 matches, so the
-  computer installs exactly the captured version. The bundle does not contain
-  the package.
- `Packages(apt=[...])` with the first alternative of each of the file's
-  Depends and Pre-Depends entries, without version constraints or `:any`
-  qualifiers, then the library packages the capture found, since a vendor's
-  binary may load libraries its Depends leaves out.
- `run=[RunScript(script="install-package.sh")]`, a script the export writes
-  into the environment folder. agentenv runs it as root from the app's folder
-  once the apt packages are installed and the download is in place, with the
-  network off: it runs `dpkg -i` on the download and then removes it.
-
-The bundle supports only the file's architecture. Vendor sites often refuse
-automated downloads, as varicad.com does, so the URL may need to point at a
-copy you keep, such as a private mirror; you must be allowed to use that copy,
-and the package's licence, such as a 30-day trial's terms, is yours to check.
-The README and the result's limitations say so.
-
-The export refuses a package no recorded repository lists when `--package-url`
-is missing, saying to capture with `--package-file` if the capture lacks it. It
-also refuses `--package-url` when the capture recorded no package file, giving
-the capture's `package_file_reason` when there is one; when the archive or a
-declared vendor repository installs the package already; when the URL is not
-written as `http://` or `https://` or holds a user name or password; and when
-the file is built for an architecture other than `amd64`, `arm64` or `all`.
-
-## Typed views
-
-The views follow the [state view](desktop-application-state.md)'s formats and
-shapes: SQLite tables (at most 64 ordinary tables, `tables_truncated` past
-that, and per table `columns`, `primary_key`, at most 500 `rows` and
-`truncated`, with blobs, unsafe integers and text that is not UTF-8 tagged as
-REA tags them), JSON, XML as `{root, truncated}` with REA's node, depth and
-whitespace rules and its `doctype` when the document declares one, key file
-groups, text as
-`{lines, line_count, truncated}` split on `\n` and `\r\n`, and zip archives
-as their entries, read with Python's `zipfile` from the file in place, with
-REA's entry, size, compression ratio and archive limits and its wording for an
-entry it does not read. The module reads the central directory itself, as REA
-does, and shows `zipfile` only the records it lists, reading each entry in
-bounded chunks no further than a byte past its declared size. A JSON file
-holding a number JavaScript cannot read exactly, such as an integer above 2^53,
-or whose retained value nests more than 500 levels deep, gets an `error` instead of a view, as in
-REA. Duplicate keys keep their last value before the depth check. Text that is not one JSON
-document, such as JSON Lines, stays text. Format detection follows REA's
-rules. Files larger than 64 MiB get an `error` instead of a view
-and are not read. XML is read with Python's `expat` twice: with namespace
-processing, which refuses what REA's parser refuses, such as an undeclared
-prefix, then without it, so element and attribute names keep the prefixes the
-document spells and namespace declarations stay attributes, as in REA's view;
-text splits into nodes where REA's splits it, at CDATA sections, comments and
-processing instructions. Both passes read a DOCTYPE as REA does: with
-parameter entity parsing off, so the DTD it names is never read, and handlers
-that refuse an internal subset, an external entity and an entity expat would
-skip; the first pass also checks each start tag for a reference to an
-undeclared entity, which expat drops from an attribute value without a word
-when a DOCTYPE names a DTD. Known differences remain:
-
- dconf databases are reported as binary, since REA reads them with `dconf`;
-  inside an archive, one is `dconf` with an error, as in REA.
- Zip entry names: a name in an Info-ZIP Unicode Path extra field is used only
-  where Python's `zipfile` reads it (3.12 and later), and an entry whose local
-  header names it differently from the central directory is damaged rather
-  than read.
- SQLite databases are read in place, read-only, rather than from a staged copy;
-  a write lock the running app holds is waited out for a quarter of a second
-  and then gives the file an `error`, and so does a table or column name that
-  is not UTF-8.
-
-The seed is the user's real data. Keep the bundle local and do not publish it.
-The class was checked against agentenv-framework 0.9.1431 with
-`python -m agentenv_protocol.computer._declare` and `agent-env run --dry-run`.
@@ -1,211 +0,0 @@
-# Desktop application state
-
-`rea inspect-desktop-application-state <capture-folder>` reads a folder written
-by [desktop application capture](desktop-application-capture.md) and describes
-the application's state: which observed files are the application's, what each
-retained version contains as typed JSON, and how each file changed between
-checkpoints. It reads only the capture folder; the application is not run
-again.
-
-```sh
-rea inspect-desktop-application-state ./mousepad-capture --format json
-```
-
-The result is Evidence with operation `inspect_desktop_application_state` and
-predicate type `rea.desktop-application-state`. Its confidence is `inferred`,
-because roles come from heuristics; the views themselves are read from the
-retained bytes, which are checked against their SHA-256 before use.
-
-## Paths and roles
-
-The view covers every file retained at the baseline and every file that
-changed later. Each path records the evidence the capture holds about it:
-
-| Reason                   | Meaning                                                                   |
-| ------------------------ | ------------------------------------------------------------------------- |
-| `state_directory`        | It lies in one of the application's state directories, in either spelling |
-| `opened_by_application`  | An application process held it open during a sample                       |
-| `named_in_window_title`  | An application window title spelled its name or `~/` path on its own      |
-| `selected_path`          | It lies under a `--state-path` or absolute `--argument` of the capture    |
-| `dconf_application_keys` | It is a dconf database holding groups whose path names the application    |
-| `desktop_service`        | It lies where desktop services and toolkits keep shared files, or caches  |
-| `desktop_trash`          | It lies in the desktop Trash, `~/.local/share/Trash`                      |
-
-A folder beside a state directory whose name differs from it only in letter
-case counts as that state directory, so a profile the application first
-creates during the capture, such as GIMP's `~/.config/GIMP` beside the
-candidate `~/.config/gimp`, is its state too.
-
-The role follows from the reasons, in this order: `shared_desktop` for a file
-in the desktop Trash, which the user deleted, whatever else names it;
-`application_state` for application keys in dconf, or a state directory outside shared desktop
-locations; `document` for a file named in a window title or selected by the
-caller, even if the application holds it open; `application_state` for another
-open file outside shared locations; `shared_desktop` for other files in shared
-locations; `unrelated` otherwise. A window title names a file only when no
-other file name character adjoins the name, so `day.txt` does not match
-`today.txt - Notes`.
-
-Application names, which select dconf groups, come from the package, the
-executable, the desktop entry's id and `StartupWMClass`, and the window match.
-The entry's display name is left out, since a generic name such as `Settings`
-would claim other applications' groups.
-
-## Versions and views
-
-Each path lists its versions: the baseline, then its state after each
-checkpoint where it, or a database's `-wal` or `-journal` file, changed. A
-checkpoint that leaves an absent file absent adds no version. A file's state
-at any checkpoint is its last version recorded at or before it, which is how
-the [export](desktop-application-export.md#the-seed-checkpoint) and the
-[task draft](desktop-application-tasks.md) read it at the seed and end
-checkpoints they are given; `capture.checkpoints` lists the names in order.
-Views hold the captured bytes as they are, the capture host's name and user
-included; the export removes those from the bundle. A version records
-whether the file was present, the SHA-256 of its retained bytes, and a view:
-
-| Format    | Detected by                                                            | View                                                                                   |
-| --------- | ---------------------------------------------------------------------- | -------------------------------------------------------------------------------------- |
-| `sqlite`  | The `SQLite format 3` header                                           | Every ordinary table's columns, primary key and up to 500 rows                         |
-| `dconf`   | The `GVariant` header                                                  | Groups whose path names the application, plus the names of the other groups            |
-| `zip`     | A zip local file header, `PK\x03\x04`, whatever the name               | Its file entries in archive order, each with its own format and view                   |
-| `json`    | A `.json` name or a leading `{` or `[` that parses                     | The parsed value, from files up to 4 MiB nested up to 500 levels                       |
-| `xml`     | An XML name or declaration that parses                                 | An element tree (`name`, `attributes`, `children`); text kept exactly, DTDs never read |
-| `keyfile` | Only `[group]`, `key=value` and comment lines, with at least one group | Groups of `key` → string value, from files up to 4 MiB                                 |
-| `text`    | Other UTF-8 text                                                       | Lines, up to 5,000                                                                     |
-| `binary`  | NUL bytes or invalid UTF-8                                             | None                                                                                   |
-
-A JSON value holding a number JavaScript would round, such as an integer above
-2^53, is not read rather than shown rounded.
-
-An XML view names elements and attributes as the document spells them, prefix
-included: a saved Inkscape drawing's root is `svg`, in its default namespace,
-with `sodipodi:docname` and the declarations `xmlns` and `xmlns:sodipodi`
-among its attributes, and a Writer paragraph is `text:p`. An element's
-`children` hold its elements and text in order, text split where a CDATA
-section, comment or processing instruction falls. Whitespace-only text between
-child elements is formatting, and dropped, in an element that holds no other
-text, unless `xml:space="preserve"` applies; in mixed content, an element with
-text of its own beside its children such as a paragraph split into runs, it is
-kept, so `<p>Meet on <s>Sunday</s> <s>evening</s></p>` keeps the space between
-the runs. Whitespace here is XML's: space, tab, carriage return and line feed;
-a no-break space is text. The view keeps up to 5,000 nodes, comments and
-processing instructions counted, nested up to 64 levels, and sets `truncated`
-when it leaves some out.
-
-A document that begins with a DOCTYPE naming its DTD, as AbiWord's `.abw`
-does, reads as the same element tree, and the view records the declaration
-beside `root`, its public identifier normalized as XML matches it:
-
-```json
-{
-  "doctype": {
-    "name": "abiword",
-    "public_id": "-//ABISOURCE//DTD AWML 1.0 Strict//EN",
-    "system_id": "http://www.abisource.com/awml.dtd"
-  },
-  "root": { "name": "abiword", "attributes": {}, "children": [] },
-  "truncated": false
-}
-```
-
-An identifier the DOCTYPE leaves out is `null`, and a document without one
-has no `doctype`. The DTD is never fetched or read, so it adds no default
-attributes and declares no entities. A DOCTYPE with an internal subset
-(`<!DOCTYPE a [ … ]>`), which could declare entities, is not read as XML, nor is
-a document that refers to any entity but XML's five (`&amp;`, `&lt;`, `&gt;`,
-`&apos;`, `&quot;`); such a file is text.
-
-Exported XML views use REA's same formatting-whitespace classification, so
-retained XML text and the task checks that address it stay aligned.
-
-SQLite databases are read through REA's SQLite worker from a private copy,
-with any retained `-wal` or `-journal` file staged beside it; the worker
-accepts an inactive rollback journal and refuses a hot one. A version is not
-read when its `-wal` or `-journal` file existed but was not retained, or when
-the capture did not record whether either existed, since the database alone
-could misstate its committed rows. The capture records them under its content
-roots, which include both beside a database selected on its own, when its
-baseline walk listed every directory, read every path, entered no other
-device, did not stop early and recorded what it left out, and wherever they change; an excluded log, and any elsewhere, is
-unknown, since an unchanged file and a missing one look alike. A table
-that cannot be read keeps its `error` in place of its rows, and changes to that
-database are marked incomplete. dconf
-databases are read with `dconf dump /` against a private file profile, so the
-live database and the dconf service are not touched; this needs `dconf-cli`, or
-`REA_DCONF_COMMAND`.
-
-A version has a `view_error` when its bytes were not retained, are over the 64
-MiB read limit, are missing or no longer match their digest, exceed a format's
-limit above, or its reader failed.
-
-## Archives
-
-Many applications save a document as a zip archive of XML and other files:
-FreeCAD's `.FCStd` and `.FCBak`, OpenDocument (`.odt`, `.ods`, whose
-`content.xml` is the document), Office Open XML, EPUB and JAR. Such a file is
-`zip`, and its view lists its file entries in archive order, leaving out
-directories: an entry whose name ends in `/`, or whose attributes mark a Unix
-directory or, from an MS-DOS host, the directory attribute:
-
-```json
-{
-  "entries": [
-    {
-      "name": "Document.xml",
-      "size": 11923,
-      "sha256": "…",
-      "format": "xml",
-      "view": {
-        "root": { "name": "Document", "attributes": {}, "children": [] },
-        "truncated": false
-      },
-      "view_error": null
-    }
-  ],
-  "entry_count": 15,
-  "truncated": false
-}
-```
-
-Each entry's bytes are read from the archive's verified bytes in memory,
-checked against its CRC-32 and declared size, and given a `format` and `view`
-by the rules and limits above, with the entry's name in place of a file name.
-Nothing is extracted to disk. An entry has a `view_error`, with `sha256`,
-`format` and `view` null, when it is encrypted, compressed other than stored or
-deflated, larger than 16 MiB, more than 100 times its compressed size, past the
-64 MiB read from one archive, or its data is damaged. A SQLite or dconf
-database, or an archive, inside an archive keeps its format and `sha256` and
-has a `view_error` instead of a view: it is not read. The view lists at most
-1,000 entries; `entry_count` counts them all, and `truncated` is true when some
-are not listed. REA reads the central directory itself, a record at a time,
-through the Zip64 end record whenever a Zip64 locator precedes the end record,
-as Python's `zipfile` does, and hands the zip reader only the records it lists,
-so an archive of hundreds of thousands of entries costs no more to read
-than one of a thousand. An archive whose central directory cannot be read has a
-`view_error` of its own.
-
-## Kinds of change
-
-Between consecutive versions a change is `created`, `deleted`, or a
-format-specific kind with what was added, removed and changed (up to 100 of
-each, with counts):
-
- `lines` for text: lines added and removed, as a multiset.
- `values` for JSON and XML: JSON pointers to values, containers included, so
-  an array that becomes an object with the same members is changed. A pointer
-  longer than 4096 characters is counted but not listed.
- `values` for zip archives too, with array members named by
-  [selectors](desktop-application-tasks.md#pointers-and-selectors) rather than
-  positions wherever a selector names one member in both versions: entries by
-  name, as `/entries/[name=Document.xml]`, and XML elements by tag and an
-  attribute, as `/view/root/children/[name=Object][@name=Hole]`, so an object
-  inserted before another does not shift it. A comparison is incomplete when
-  either view leaves out entries, or an entry's view is missing or truncated.
- `keys` for key files and dconf: `group/key`, with `~` and `/` in the key
-  written `~0` and `~1` as in a JSON pointer, so `[a/b]` `c` and `[a]` `b/c`
-  stay apart.
- `rows` for SQLite: `table:` and the row's primary key, or the whole row when
-  the table has none.
- `content` for binary files, and `unreadable` when either version has no
-  view.
@@ -1,343 +0,0 @@
-# Desktop application tasks
-
-A [desktop application export](desktop-application-export.md) can carry one
-task: a prompt for a computer-use agent and checks that grade what the agent
-left in the application's files. An agent, not REA, writes the prompt and the
-checks from the change the capture recorded. REA validates the task against
-the capture and keeps it only when its checks fail on the seed and all pass on
-the captured end state. REA runs no model and no code the agent wrote: the
-checks are declarative, and the exported verifier evaluates them the same way
-REA does.
-
-```sh
-rea describe-desktop-application-task ./mousepad-capture --format json > draft.json
-# edit the draft's task into task.json: a name, the user's request, the checks
-rea export-desktop-application ./mousepad-capture ./mousepad-bundle --task task.json
-agent-env run ./mousepad-bundle --task add-milk --agent claude-code
-```
-
-## Describe the change
-
-`rea describe-desktop-application-task <capture-folder>` reads the capture and
-its [state view](desktop-application-state.md) and returns Evidence with
-operation `describe_desktop_application_task` and predicate type
-`rea.desktop-application-task-draft`:
-
- `application`: the environment name the export would use, the title and the
-  window class.
- `owned_paths`: the paths the export owns, the only ones whose files the
-  app's `data/get` serves and checks can read.
- `checkpoints`: the two checkpoints compared, `baseline` for the seed and
-  `final` for the end. They are the capture's first and last unless
-  `--seed-checkpoint` and `--end-checkpoint` name others, as for the
-  [export](desktop-application-export.md#the-seed-checkpoint), which takes
-  the same options; a name the capture does not hold, or an end before the
-  seed, is refused.
- `files`: each file under them whose state differs between those
-  checkpoints, with its home path, role, its versions at both (`baseline` and
-  `final`, the last recorded at or before each) and the net change between them, from the state view's own diff (`lines`, `values`,
-  `keys` or `rows` with what was added, removed and changed, or `created`,
-  `deleted`, `format`, `content`, `unreadable`; `content` also when the
-  views hold only part of a file and match while the file changed). A
-  database is compared by its rows, since its hash leaves out the `-wal`
-  file. Text changes list each line
-  once and add `line_counts`, the lines found at both ends whose number of
-  occurrences changed. Views appear only for the files the suggestions cover,
-  with arrays past 200 items and strings past 2,000 characters cut
-  (`view_cut`).
- `task`: a draft with the name `change`, a placeholder prompt the export
-  refuses, and suggested checks derived from the net change of the files with
-  role `document`, or of the app's own state files when no document changed.
-  A text file gains `lines_present` for its new lines and `lines_absent` for
-  lines it lost (when either is at most ten), and `line_count` for each line
-  holding a letter whose count changed; JSON and key files gain
-  `value_equals` and `value_absent` by pointer; SQLite tables gain rows added,
-  changed and removed, by primary key, and their new row count. An XML file,
-  and the JSON, key file and XML views of a zip archive's entries, gain checks
-  by [selectors](#pointers-and-selectors) and never through an element by
-  position: in XML, first [`text_equals`](#whole-text) for each element whose
-  text changed, then an element added whole that it exists, one removed whole
-  that it is absent, then values changed, added and removed, an entry or a
-  JSON value added whole through its members, and an empty array or object as
-  it is. The text check names the paragraph rather than a run inside it: it
-  goes up from an element sitting in its parent's text, and from one named by
-  its tag or position alone to the nearest ancestor named by an attribute, as
-  AbiWord's `p` by its `xid`; the text nodes and runs inside it get no other
-  check, but an element holding no text that is added or removed there, such
-  as an image or a line break, keeps its own, since the text check never
-  reads it. Whitespace an app lays out between elements is not checked, and
-  values that look like a time the app stamps, in ISO 8601 or as C's
-  `asctime` writes it (`Thu Nov  5 09:20:31 2026`), are left out.
-
-The suggestions are a starting point. Keep the ones that say what the user
-did; drop the ones that only follow from how the app saves its file. A LibreCAD
-capture that added four holes to a drawing rewrote it from DXF R12 to DXF 2007,
-so most of its lines changed; the draft suggests counts of `SECTION`, `ENDSEC`
-and `CIRCLE`, and only `CIRCLE` going from 5 to 9 is the user's change.
-
-## The task file
-
-```json
-{
-  "name": "add-milk",
-  "prompt": "Add buy milk to my to-do list in Mousepad and save it.",
-  "checks": [
-    {
-      "id": "milk",
-      "kind": "lines_present",
-      "file": "Documents/todo.txt",
-      "lines": ["buy milk"]
-    }
-  ]
-}
-```
-
-`name` is a portable bundle name other than `smoke` (lowercase letters, digits
-and hyphens); `prompt` is what the user asks for; `checks` holds 1 to 32
-checks. Each check has a `kind`, a `file` given as a path under the home such as
-`Documents/todo.txt`, and an optional `id` (`check-1`, `check-2` and so on by
-position otherwise). A check reads the typed view `data/get` returns for that
-file, in the shapes of the state view.
-
-| Kind            | Fields                                                       | Passes when                                                              |
-| --------------- | ------------------------------------------------------------ | ------------------------------------------------------------------------ |
-| `file_present`  |                                                              | The file exists                                                          |
-| `file_absent`   |                                                              | The file does not exist                                                  |
-| `lines_present` | `lines`                                                      | Every listed line is a whole line of the text view                       |
-| `lines_absent`  | `lines`                                                      | None of the listed lines is                                              |
-| `line_count`    | `exact` or `contains`; `equals`, `at_least` or `at_most`     | The number of lines equal to `exact`, or holding `contains`, compares so |
-| `value_equals`  | `pointer`, `value`; optional `tolerance`                     | The pointer names a value equal to `value`, or within `tolerance` of it  |
-| `value_absent`  | `pointer`                                                    | The pointer names no value                                               |
-| `text_equals`   | `pointer`, `value`; optional `normalize_whitespace`          | The XML element's [whole text](#whole-text) equals `value`               |
-| `text_contains` | `pointer`, `value`; optional `normalize_whitespace`          | The XML element's whole text holds `value`                               |
-| `row_present`   | `table`, `where`                                             | A row of the SQLite table has every column in `where` equal              |
-| `row_absent`    | `table`, `where`                                             | No row does                                                              |
-| `row_count`     | `table`; optional `where`; `equals`, `at_least` or `at_most` | The number of rows, or of rows matching `where`, compares so             |
-
-The rules both evaluators follow:
-
- An absent file reads as empty: no lines, values or rows. So `lines_absent`,
-  `value_absent` and `row_absent` pass on it and a count is 0.
- A file that has no view (binary, over the read limit, or unreadable) fails
-  every check but `file_present` and `file_absent`. Line checks need a text
-  view, row checks a SQLite view and text checks an XML view, in a file or an
-  archive entry; another format fails.
- Equality is JSON equality: numbers by value, never a boolean for a number,
-  objects by their keys whatever their order, arrays in order.
- Pointers follow RFC 6901 (`~1` for `/`, `~0` for `~`) and must start with
-  `/`; on an array a segment may be a selector, below. Key files read as
-  `{"groups": {"GROUP": {"KEY": "VALUE"}}}`, so a setting is
-  `/groups/GROUP/KEY`; XML as `{"root": {"name", "attributes", "children"}}`;
-  SQLite as `{"tables": {"TABLE": {"columns", "rows"}}}`; a zip archive as
-  `{"entries": [{"name", "format", "view", …}]}`.
- With `tolerance`, a non-negative number, `value` must be a number, and the
-  value found passes when it is a number, or a string that is a decimal
-  numeral such as `"5.0000000000000000"`, at most `tolerance` from `value`.
-  `tolerance: 0` compares numerically, so `"1.2500"` equals `1.25`. Anything
-  else fails as not a number.
- `contains` matches a line that holds it anywhere, case and all. Checks take
-  no regular expressions: a pattern run on what the agent wrote could stall
-  the verifier, and JavaScript and Python read some patterns differently.
- A check decided by what a view leaves out (`lines_absent`, `value_absent`,
-  `row_absent`, the counts, `value_equals` of a whole object or array, and
-  the text checks of an element) fails when that view is truncated; a check
-  satisfied by what the view holds is decided on it.
-
-The export refuses, naming the check, a file outside the owned paths, a file
-spelled with a leading slash, `.` or `..`, a pointer into a file that is text
-at the seed, as the bundle ships it, or at the end checkpoint, the empty
-pointer (the whole file), a value that names the captured home, or the
-capture host's name or `user@host` anywhere (which the
-[export removes from the seed](desktop-application-export.md#host-name-and-user)), a
-`tolerance` with a value that is not a number, an empty `text_contains`
-value, or one of only whitespace with `normalize_whitespace`, and a value that
-looks like a date and time, in ISO 8601 or `asctime`'s form. Other volatile
-content, such as a
-counter the app bumps on every save, is for the author to leave out.
-
-## Pointers and selectors
-
-An app that rewrites a document moves things: FreeCAD 1.0 records more
-properties than 0.21, so a hole's radius sits at another position among its
-siblings, and a plate's entry moves once a hole is added before it. A pointer
-segment applied to an array may therefore name a member by what it holds
-rather than by its position:
-
- `[KEY=VALUE]` names the member whose string field `KEY` is `VALUE`, such as
-  a zip entry by `[name=Document.xml]` or an XML element by its tag,
-  `[name=Object]`.
- `[@KEY=VALUE]` names the member whose `attributes` hold `KEY="VALUE"`, as
-  the XML view keeps an element's attributes.
- Conditions can follow one another, `[name=Object][@name=Hole]`, and all must
-  hold. They compare strings only, the selector is escaped like any pointer
-  segment (`~1` for `/`), and a value cannot hold `][`.
-
-A selector must name exactly one member. When several match, or none does
-before the last segment, the check fails and says which selector matched what.
-When the last segment's selector matches none, the pointer names no value:
-`value_absent` passes, which is how a check says an element was removed, and
-`value_equals` fails. On an object, a bracketed segment is an ordinary key.
-
-A FreeCAD task that checks the user cut a 10 mm hole through the plate, in
-FreeCAD 0.21 and 1.0 alike:
-
-```json
-{
-  "name": "cut-hole",
-  "prompt": "Cut a 10 mm hole through the middle of the plate and save it.",
-  "checks": [
-    {
-      "id": "cut",
-      "kind": "value_equals",
-      "file": "Documents/plate.FCStd",
-      "pointer": "/entries/[name=Document.xml]/view/root/children/[name=Objects]/children/[name=Object][@type=Part::Cut]/attributes/type",
-      "value": "Part::Cut"
-    },
-    {
-      "id": "radius",
-      "kind": "value_equals",
-      "file": "Documents/plate.FCStd",
-      "pointer": "/entries/[name=Document.xml]/view/root/children/[name=ObjectData]/children/[name=Object][@name=Hole]/children/[name=Properties]/children/[name=Property][@name=Radius]/children/[name=Float]/attributes/value",
-      "value": 5,
-      "tolerance": 0.01
-    }
-  ]
-}
-```
-
-Before the edit the archive has no `Part::Cut` and no `Hole`, so both checks
-fail on the seed; after it, `Radius` is `"5.0000000000000000"` and both pass.
-A check decided by what a view leaves out depends, in an archive, on the entry
-its pointer goes into: it fails when that entry's view is missing or
-truncated, or when the entry is not listed and the listing is truncated. A
-selector must see every member to know it names one, so a check whose pointer
-searches an array the view may hold only part of fails as undecided: any array
-of a truncated XML view, of a truncated entry's view, or the listing when it
-is cut. A position is decided on what the view holds. Like a file, an entry
-that has no view (binary, not read, or a database or archive inside the
-archive) fails every check into its `view`; its `null` there is no value, while
-an entry holding the JSON document `null` reads as `null`. Checks on its `name`,
-`size`, `sha256` and `format` still read.
-
-XML that uses namespaces is named as the document spells it, in both
-evaluators: an element or attribute by its prefixed name, such as `text:p`
-or `inkscape:label`, an element in a default namespace by its bare name, such
-as `svg`, and namespace declarations as the attributes `xmlns` and
-`xmlns:PREFIX`. Text is a string among an element's `children`. These checks
-hold a poster's headline in an Inkscape SVG and a date in a LibreOffice Writer
-document:
-
-```json
-[
-  {
-    "id": "headline",
-    "kind": "value_equals",
-    "file": "Pictures/poster.svg",
-    "pointer": "/root/children/[name=g][@inkscape:label=Layer 1]/children/[name=text][@id=headline]/children/[name=tspan]/children/0",
-    "value": "Summer Bake Sale"
-  },
-  {
-    "id": "date",
-    "kind": "value_equals",
-    "file": "Documents/flyer.odt",
-    "pointer": "/entries/[name=content.xml]/view/root/children/[name=office:body]/children/[name=office:text]/children/[name=text:p][@text:style-name=Subtitle]/children/0",
-    "value": "Monday 24 November"
-  }
-]
-```
-
-Inkscape writes a line of text as a `tspan` inside its `text` element, and
-Writer keeps a paragraph's style in `text:style-name`. A prefix is the one the
-document uses, so a check names the prefixes the app writes.
-
-## Whole text
-
-A text node is only the stretch of text between two pieces of markup, and
-apps split a paragraph into runs as they save it. AbiWord wraps text typed
-into a reopened document in `c` elements, so changing a time to `3:30` saves
-`<p>The team meeting starts at <c>3</c>:<c>30</c> in room 4.</p>`; Writer,
-which records revision IDs by default, writes text typed in one session as
-`text:span` runs. A `value_equals` on the paragraph's `children/0` then reads
-`"The team meeting starts at "` and fails. `text_equals` and `text_contains`
-read the element's whole text instead:
-
-```json
-{
-  "id": "time",
-  "kind": "text_equals",
-  "file": "Documents/meeting.abw",
-  "pointer": "/root/children/[name=section]/children/[name=p][@xid=3]",
-  "value": "The team meeting starts at 3:30 in room 4."
-}
-```
-
- The pointer names an element of an XML view, in a file or in an archive
-  entry's `view`, or a text node or attribute value in one, whose text is its
-  value. Another format, a pointer into an archive outside an XML entry's
-  view, or any other value fails, an element's `name` and the `doctype`'s
-  fields included: they are strings of the view, not text of the document.
- An element's text is XPath's `string()` of what the view keeps: every text
-  node in it and in its descendants, CDATA included, in document order, with
-  nothing between them. The view drops whitespace-only text between child
-  elements only in an element that holds no other text, outside
-  `xml:space="preserve"`, so the space between two runs of a paragraph is
-  part of its text. Elements that stand for characters, such as Writer's
-  `text:s`, `text:tab` and `text:line-break`, add none.
- `text_equals` passes when the text equals `value` exactly, case and all;
-  `text_contains` when it holds `value`, as a time within a sentence, so the
-  check holds whatever the rest of the sentence says.
- `normalize_whitespace: true` collapses each run of XML whitespace (space,
-  tab, carriage return, line feed) in both the text and `value` to one space
-  and trims both ends before comparing, as XPath's `normalize-space()` does,
-  for an app that reflows text or a value written across lines. A no-break
-  space is not whitespace there.
-
-## Validation and export
-
-`rea export-desktop-application <capture> <directory> --task <task.json>`
-evaluates the checks on the capture's state view: on each file as it was at
-the seed checkpoint, which is the seed, as the bundle ships it with the
-capture host's name and user removed, and at the end checkpoint, the
-captured end state. Those are the capture's first and last checkpoints unless
-`--seed-checkpoint` and `--end-checkpoint` name others.
-It refuses a task whose every check passes on the seed, and a check that fails
-on the end state, with that check's reason. Only a failure on what the seed's
-view shows counts: a task whose checks fail on the seed only because a view
-could not be read or may have left out what they look for, such as a line past
-the 5,000 a text view keeps, is refused, naming each failure. A capture yields
-one task, so the option is taken once. The result's `task` names the task, its
-number of checks and those that fail on what the seed shows. A refused task
-writes no bundle.
-
-The bundle then holds, besides the app and `tasks/smoke.json`:
-
-| Path                               | Contents                                                                                                               |
-| ---------------------------------- | ---------------------------------------------------------------------------------------------------------------------- |
-| `tasks/<name>.json`                | Deploy the app, deploy the agent and its skills, record the screen, prompt the agent, run the verifier, stop recording |
-| `artifacts/<name>-check/verify.py` | Reads the app's `data/get` through the computer and evaluates the checks, one result per check                         |
-| `evals/<env>.toml`                 | The task, so a run of the bundle runs it; the smoke task runs with `--task smoke`                                      |
-
-The verifier finds the app among the computer's child environments, calls its
-`data/get` under the run's grant of the computer's control token, and reads
-the `state` data part. It raises when the app cannot be reached, so the run
-fails rather than scoring the agent. The README lists the task, its prompt, its
-checks and the recipe below.
-
-## Solve rate
-
-REA does not run agents. To measure how often an agent solves the task, run it
-k times, three by default, and count the runs whose summary line says
-`passed`:
-
-```sh
-for run in 1 2 3; do
-  agent-env run ./mousepad-bundle --task add-milk --agent claude-code --model MODEL
-done
-```
-
-The agent defaults to Claude Code and the model is the caller's choice (Claude
-Sonnet 5.5 is a reasonable reference). A run reported as `scored below 1`
-failed the checks and counts as a miss; one reported as `failed` did not finish,
-as when the computer or the app could not be reached, and is run again rather
-than counted. Each run's instance keeps the verifier's results per check under
-`verifications`.
@@ -110,15 +110,6 @@ not establish full metadata validity or correspondence to a native binary;
 version 24 inspection still applies only to supported header layouts. See
 [IL2CPP metadata](il2cpp-metadata.md).

-In a managed directory with a Unity Mono witness, `Assembly-CSharp.dll` and
-`Assembly-CSharp-firstpass.dll` get an `inspect_managed_members` probe listed
-first; project-named asmdef assemblies keep only the ordinary managed probes.
-The same probe is offered for those names in `Managed/` of a
-`<Product>_BackUpThisFolder_ButDontShipItWithYourGame` folder (or when that
-folder is the root); whether its IL matches the shipped IL2CPP code is unknown.
-Point the scan at the game folder: a root that is the `<Product>_Data` or
-`Managed` folder itself has no Mono witness path and gets no member probe.
-
 Candidates are derived or inferred from these facts and do not prove loading or
 execution. BepInEx, MelonLoader, Easy Anti-Cheat and BattlEye labels identify
 path conventions only; runtime presence stays unknown. No bypass is provided.
@@ -1,199 +0,0 @@
-# Desktop build computer
-
-A build computer is a local agentenv computer that an agent drives while it
-builds a desktop app environment. Claude Code cannot attach a new MCP server
-in the middle of a session, so REA keeps the computer up and forwards the
-agent's computer-use actions to it through three MCP tools:
-
-| Tool                    | What it does                                                                               |
-| ----------------------- | ------------------------------------------------------------------------------------------ |
-| `start_build_computer`  | Starts a computer from a request or a bundle folder; returns its id and a first screenshot |
-| `act_on_build_computer` | Sends one action to the computer's driver and returns the driver's answer, images included |
-| `close_build_computer`  | Tears the computer down, by agentenv's teardown or by removing its sandbox's containers    |
-
-The tools are MCP-only, like the debugger sessions: the computer lives as long
-as the REA MCP server that started it, or until it is closed. Capturing the
-app, exporting its bundle and witnessing the task on such a computer are in
-[Building and witnessing an environment](desktop-build-witness.md).
-
-## Requirements
-
- Docker, and an agentenv-framework install whose `agent-env` program is named
-  by the absolute `REA_AGENT_ENV_COMMAND`. Bundles target agentenv
-  0.9.1431. REA runs its helper, `bridge/agentenv/computer.py`, with that
-  runner's Python: the interpreter on the program's `#!` line, or the
-  `python3` beside it in its virtual environment.
- `REA_DOCKER_COMMAND`, the absolute path of the Docker CLI, lets REA remove a
-  computer whose agentenv teardown was not confirmed. Without it, REA names the
-  command to run instead.
- For a request, `REA_BUILD_COMPUTER_REA_ARCHIVE`: the absolute path of a tar
-  archive of a runnable REA, with its production dependencies, whose one top
-  folder holds `scripts/rea.mjs`. The computer runs REA from it. From a
-  checkout, `npm run pack:build-computer-runtime -- /path/to/rea-prod.tar.xz`
-  writes one: `npm pack`, its package folder as
-  `rea-prod` with the lockfile, `npm ci --omit=dev --omit=optional`, then
-  `rea-prod` as `.tar.xz`.
-
-Set these where the MCP server starts; a shell export does not reach a server
-that is already running.
-
-## Start a computer
-
-From a request, REA renders a bundle in a private temporary folder: a computer
-app on the `ubuntu-24.04` base with the `reference` driver that installs the
-app, opens it on demand with `gtk-launch <desktop entry>` from the computer
-user's home, so its open and save dialogs start there rather than in the
-framework's folder for the app, and keeps no seed and no data hooks. The app is not open when the computer starts: agentenv lists it
-in the desktop's Applications menu under Other by the environment's name, such
-as `mousepad`, and that entry launches it through the app's server.
-
-When the app is Electron, set `electron` to true. The install rewrites that
-desktop entry's command with the same policy an export uses: `--no-sandbox`
-immediately after the program, unless the command already has it. The
-computer's container does not grant the user namespaces Chromium's sandbox
-needs, and Electron exits without the flag. With the rewritten command, the
-Applications menu entry can open the app.
-
-```json
-{
-  "source": {
-    "kind": "request",
-    "desktop_entry": "org.xfce.mousepad",
-    "window_class": "Mousepad",
-    "install": { "kind": "archive", "package": "mousepad" }
-  }
-}
-```
-
-`install` takes one of:
-
-| `kind`           | Installs                                                                                                   |
-| ---------------- | ---------------------------------------------------------------------------------------------------------- |
-| `archive`        | `package` from the Ubuntu 24.04 archive, on amd64 and arm64                                                |
-| `apt_repository` | `package` from the repository at `uri` with `suite` and `components`, trusting the key file `key_file`     |
-| `package_file`   | The `.deb` at `url`, checked against `sha256`, for one `architecture`, after its apt `dependencies` are in |
-
-Build steps run with the network off, so a `.deb`'s dependencies must be
-listed. The bundle adds REA in a build-only layer: Node.js
-24.22.1, downloaded per architecture and checked against its release checksum,
-and REA from `REA_BUILD_COMPUTER_REA_ARCHIVE`, both unpacked into `/opt/rea` by
-a root build step, with `node` and `rea` on `PATH`. An exported bundle carries
-none of it.
-
-From a bundle folder, such as one `export-desktop-application` wrote, REA
-starts that bundle's `tasks/smoke.json` as it is:
-
-```json
-{ "source": { "kind": "bundle", "path": "/home/ada/mousepad-bundle" } }
-```
-
-REA runs its helper with `PYTHONDONTWRITEBYTECODE=1`, which agentenv's own
-import of the bundle's app class inherits, so a start leaves no `__pycache__`
-in the folder and its files stay as they were shared.
-
-REA runs the deploy with `run_bundle(keep=True, emulate=False)` on the local
-sandbox provider, so only the host's own architecture is built. The first start
-of a bundle builds its image and can take minutes; later starts reuse it.
-While it waits, REA sends an MCP progress notification every five seconds with
-agentenv's latest line, so a client that resets its request timeout on
-progress keeps waiting. REA then waits until the computer's readiness checks
-pass and opens one MCP session to its driver. Readiness can pass before the
-desktop has drawn, so REA takes a whole-screen PNG screenshot every 500 ms
-while it is one colour throughout. The retries share 10 s, each given only
-what is left of it, and when that runs out REA returns the latest frame;
-progress notifications continue meanwhile. Given `screenshot` with a
-`region`, `format` or `quality`, REA then takes one with them, a `region`
-cropping that frame. The result holds
-`computer_id`, agentenv's `sandbox_id`, the environment name or bundle folder,
-and the screenshot's frame as structured content beside its image.
-
-A failed start returns the last 16 KiB of the helper's stderr, where a failing
-build prints its error, and its exit status; a cancelled one stops the helper,
-which tears down whatever agentenv brought up. When that teardown is not
-confirmed, the error's `computer_id` names what REA keeps for
-`close_build_computer` to retry. Closing the server cancels starts still in
-progress and waits for them before closing every computer.
-
-## Act
-
-`act_on_build_computer` takes `computer_id`, an `action` and the driver's own
-arguments for `computer_<action>`, which REA passes through:
-
-| `action`     | Arguments                                                       |
-| ------------ | --------------------------------------------------------------- |
-| `screenshot` | `region`, `format` (`png` or `jpeg`), `quality`                 |
-| `click`      | `x`, `y`, `button`, `count` (2 double-clicks), `modifiers`      |
-| `drag`       | `path` of `[x, y]` points, `button`, `duration_ms`, `modifiers` |
-| `scroll`     | `direction`, `x`, `y`, `amount`, `modifiers`                    |
-| `type`       | `text`, where `\n` presses Enter and `\t` Tab                   |
-| `key`        | `keys`, one chord pressed in order, and `repeat`                |
-| `wait`       | `ms`                                                            |
-| `reset`      | `screenshot`                                                    |
-
-`reset` is not a driver tool: REA calls the app's `data/reset`, which restores
-the bundle's seed and relaunches the app, then waits until the computer's
-readiness checks pass again, sending an MCP progress notification every five
-seconds while it waits. With `screenshot: true` it then takes a screenshot; if
-that fails, the reset still counts as applied and its result has no `frame`
-but a `screenshot_error` with the computer's message. A computer started from
-a request has no data operations, so it refuses a reset.
-
-Pointer actions also take `frame_id`, `space` and `norm_scale`, and every
-action but `screenshot` takes `screenshot: true` for an image afterwards. That
-image is taken at once, so after an action that opens a menu or a window, ask
-for it with a `wait` of a few hundred milliseconds instead.
-Points are pixels of the latest frame, so take a screenshot first; with
-`space: "norm"` they are on a `0..norm_scale` grid over it. Keys are W3C names
-or one character; REA translates model spellings such as `ctrl+s`, `Return`,
-`esc` and `cmd` and leaves other names for the driver to judge. An argument the
-action does not take is refused before anything is sent.
-
-The result carries the driver's content unchanged, its text and images, after
-REA's own JSON: `action_index` and the driver's structured result. A refusal,
-such as a stale frame, is an error carrying the computer's message. A response
-larger than the MCP budget is refused with how to ask for a smaller image: a
-`region`, or `jpeg` with a lower `quality`. That error keeps REA's own result,
-`computer_id` included, as `details.result`, since the action or start has
-happened.
-
-Actions, the capture steps and the task checks on one computer run one at a
-time, in the order REA receives them; one that has to wait for the call
-before it sends an MCP progress notification every five seconds meanwhile.
-Different computers run side by side.
-
-Every action is logged on the computer in order with the arguments sent, its
-start and end and whether it was applied, refused or failed. The log keeps the
-latest 256 actions within 256 KiB of JSON, dropping the oldest first. Each
-string argument, such as `type`'s `text`, is kept to its first 1 KiB and each
-list, such as `drag`'s `path`, to its first 64 items; an entry names the
-arguments it cut in `truncated_arguments`, and the driver gets them whole. The
-log counts every action, so it says how many it dropped, and keeps the index of
-the last applied action of each kind for rules over the whole session. The log
-and the computer's recording hooks (`computer-recording/v1` start and end under
-REA's own request id, and the segments fetched through the driver's `data/get`
-one at a time, each read within its manifest size and checked against it) are
-what the witness records; they are not tools of their own. A recording larger
-than a quarter of the V8 heap is refused before any segment is read.
-
-## Close
-
-`close_build_computer` ends REA's MCP session and closes the helper's stdin,
-on which the helper runs agentenv's teardown. When agentenv confirms nothing is
-left, the result says `teardown: "agentenv"`. Otherwise REA removes the
-containers of that exact sandbox: agentenv runs a computer as
-`agent-<sandbox id>` without a label and labels its other containers
-`agentenv.sandbox=<sandbox id>`, so REA lists both with `docker ps -aq
--filter`, removes them with `docker rm -f`, and says
-`teardown: "container_label"`. When neither confirms it, the error names what
-is left and the computer stays listed, so closing it again retries. A close
-cancels the call in progress on the computer, refuses the calls waiting for
-it, and tears down once that call has ended. Closing the
-MCP server closes every computer the same way, and a helper whose REA server
-exits sees its stdin close and tears down.
-
-The control token that guards the computer's framework-only routes stays in
-REA: no result, error or log carries it. Code running in the computer as its
-user can still read it, which is acceptable for a local build.
-
-See the [specification](specs/desktop-app-environments/build-computer/spec.md)
-for scope and verification.
@@ -1,175 +0,0 @@
-# Building and witnessing an environment
-
-An agent such as Claude Code builds a desktop app environment from a request
-on a [build computer](desktop-build-computer.md): it makes the seed through
-the app, makes the change the task asks for, exports the bundle with the task
-it writes, and then witnesses the task in a fresh computer of that bundle.
-REA runs its own capture, task draft and export inside the build computer and
-grades the witness with the same checks the exported verifier runs.
-
-| Tool                       | What it does                                                                                |
-| -------------------------- | ------------------------------------------------------------------------------------------- |
-| `start_build_capture`      | Downloads the package lists as the computer's user and launches the app under REA's capture |
-| `mark_build_checkpoint`    | Takes a named checkpoint and returns the capture's acknowledgement with its counts          |
-| `stop_build_capture`       | Stops the capture and returns its checkpoints and the task draft between `seed` and `end`   |
-| `export_build_environment` | Exports the bundle with the agent's task inside the computer and copies it to a folder here |
-| `check_build_task`         | Grades a task against the app's live state; with a `stage`, files the check in the witness  |
-
-Like the computer tools, these are MCP-only and act on a `computer_id` from
-`start_build_computer`.
-
-## Build
-
-1. `start_build_computer` from a request. REA is installed in the computer.
-2. `start_build_capture`. REA writes an apt configuration under
-   `~/.rea-build/apt` and runs `apt-get update` as the computer's user, so the
-   capture finds the package's sources (`package_lists` counts the lists,
-   and `package_lists_error` gives apt's exit status and last lines when the
-   download failed; a later start runs the update again until one succeeds). It then starts `rea capture-desktop-application
-   --desktop-entry <entry>`
-   in the computer, leaving `~/.rea-build` out of every checkpoint, and returns
-   once the app's window is open, with a screenshot. For an app installed
-   from a `.deb` file, the build layer keeps that file at
-   `/opt/rea/package.deb` and the capture records it with `--package-file`. Do not open the app from
-   the menu first: the capture refuses an app whose window is already open.
-3. Make the seed through the app with `act_on_build_computer`, saving it
-   where the user keeps such files, such as `~/Documents`, then
-   `mark_build_checkpoint` `seed`.
-4. Make the change the task will ask for, save it, and
-   `mark_build_checkpoint` `end`.
-5. `stop_build_capture`. The app is closed and the capture finishes. The
-   result lists the checkpoints with their counts, the package and the
-   sources the capture found, its limitations and the draft: each file that
-   changed between `seed` and `end` with its net change, and suggested
-   checks with a placeholder prompt.
-6. Write the task: its name, the prompt in the user's own words, and checks
-   that hold after the change and not on the seed.
-7. `export_build_environment` with the task and a new or empty `directory`.
-   The export runs inside the computer with `--seed-checkpoint seed
-   --end-checkpoint end`, so it seeds what was saved at `seed`, scrubs the
-   computer's host name and user from it, and refuses a task whose checks
-   all pass on the seed. A task larger than 96 KiB as REA passes it to the
-   computer is refused before anything runs. A file moved to the desktop Trash is not seeded,
-   and the export's limitations name what the Trash held at `seed`. For a
-   `.deb` app that no apt source the capture found offers, the export takes
-   the request's URL with `--package-url`; one apt offers installs from apt. REA lists the bundle's files with their sizes
-   and SHA-256 in the computer, into a file beside the bundle that it reads
-   through `data/get`, since a large bundle's list outgrows a command's
-   output; it then brings the files back through the driver's
-   `data/get` in answers of at most 8 MiB, and checks and writes each answer
-   into the folder before asking for the next, so one answer at a time is
-   held; a failure leaves no partial folder.
-8. `close_build_computer`.
-
-A checkpoint name is lowercase letters, digits, dot, dash and underscore; the
-capture's own `baseline`, `stop`, `time-limit` and `exit` are refused, and so
-is a name already taken. The acknowledgement comes from the capture after it
-has walked the home and retained what changed: `entries` walked, `changes`
-since the checkpoint before, `retained_files` and `retained_bytes`.
-
-Each step can be asked again after its answer was lost:
-
- A start whose answer is lost, or whose window never opened, stops the
-  capture it may have left running. Until the computer confirms that stop,
-  REA keeps the capture and the next `start_build_capture` retries the stop
-  before starting another.
- A checkpoint the capture took whose acknowledgement was lost comes back
-  from the capture's own log when the same name is marked again.
- A stop whose summary or draft was not read finishes when stop is asked
-  again, and a finished stop repeats its result. The draft and the export
-  trust the checkpoints the capture's own Evidence records.
- A step that saved something, such as an export's bundle or the witness's
-  record, returns it even when its call is cancelled or the computer closes
-  as the save finishes. `start_build_capture` saves nothing, so a close or
-  cancellation during its screenshot of the opened app cancels it.
-
-The capture, the draft and the export run as the computer's user in its home,
-without any `AGENTENV_*` variable, so neither REA nor the app holds the
-computer's control token. REA sends each command through agentenv's
-`computer-exec/v1` route with that token, which stays in REA, and reads larger
-outputs, such as the draft, the export's Evidence and the bundle's file
-list, from files under `~/.rea-build` through `data/get`, since a command's
-output is capped at 1 MiB.
-
-Calls on one computer run one at a time, in the order REA receives them:
-an action, a capture step, a check or a close waits until the call before
-it on that computer has answered, and sends progress notifications while
-it waits. So a check reads the app with no action half done, and a witness
-stage is admitted, read and filed before anything else on that computer
-runs. Calls on different computers run side by side. Closing a computer
-cancels the call in progress on it and refuses the calls still waiting.
-
-## Witness
-
-Start a fresh computer from the exported folder with `start_build_computer`
-and `{"kind": "bundle", "path": ...}`; agentenv boots the app with the seed.
-Then, with the task exactly as exported:
-
-| `stage`       | Before it                                                         | Its checks must              |
-| ------------- | ----------------------------------------------------------------- | ---------------------------- |
-| `seed`        | nothing; give `directory`, a new or empty folder for the record   | fail at least once           |
-| `after_edit`  | the task done through the app from its prompt alone               | all pass                     |
-| `near_miss`   | a change that is almost right, such as a misspelled line          | fail at least once           |
-| `after_reset` | `act_on_build_computer` with `action: "reset"` as the last change | each come out as on the seed |
-
-`check_build_task` reads the app's `data/get`, takes the views it returns
-beside the files and evaluates each check with REA's evaluator, the one the
-export validates tasks with and the exported verifier mirrors, one result per
-check. Without `stage` it only grades. The `seed` stage begins a recording
-of the display under REA's own request id, one per computer; a seed check
-that fails after it, such as on a failed read of the app's state or a lost
-reply to the recording's start, can be asked again, and asks for the
-recording under the same id, which the computer answers with the recording
-it already began. The stages come in order. The edit and the near miss each
-need an applied click, drag, scroll, type or key since the stage before, with
-no reset after the last of them, since a reset puts the seed back rather than
-changing the app; `after_reset` needs the reset as the last change, and a
-reset that leaves any check unlike on the seed fails the witness, its
-stage's `remediation` naming those checks. On a computer started from a
-bundle folder, the seed refuses a task whose `tasks/<name>.json` or verifier
-in the bundle differs from what the export writes for it. A reset
-relaunches the app, and REA waits until the computer is ready again before
-answering, sending progress notifications while it waits.
-
-Only a check that fails on what the app's view shows counts as a failure. A
-check that fails because its file or table could not be read, such as an
-SQLite file locked past the reader's wait, or because what it looks for may
-lie in what its view cut, is `undecided` in its result: it shows nothing
-about the task. That covers a line `lines_present` misses in a text view cut
-at 5,000 lines, a row `row_present` misses in a table whose view keeps only
-its first rows, a `value_equals` pointer that names nothing in a truncated
-view or past a cut zip listing, and the absence checks and counts on a cut
-view. A check that passes on what the view kept stays decided, and so does a
-value found there that differs from the one expected. The result's `passed`
-and description are the exported verifier's, which has no undecided results.
-A stage that only undecided checks would settle, such as a near miss whose
-one failing check could not read its file, files nothing and is refused;
-check it again once the files read whole.
-
-A stage whose checks do not show what it must ends the witness, and so does
-`after_reset`. REA then ends the recording, fetches its segments through
-`data/get`, each checked against the recording's manifest, and writes into
-`directory`:
-
- `recording/NNNN.mp4`, the recording's segments;
- `witness.json`, REA Evidence (`rea.desktop-build-witness`) holding the
-  verdict, the stage that failed if one did, the task's name and SHA-256,
-  each stage's results with how many logged actions came before it, the
-  computer's [action log](desktop-build-computer.md#act) as it keeps it, each
-  action with its arguments, timing and outcome, with `actions_dropped`
-  counting the earliest actions it no longer keeps, and the recording's
-  segments with their sizes and SHA-256. The record's limitations say when
-  the log dropped actions or cut arguments, which each entry names in
-  `truncated_arguments`.
-
-The stages' rules read the log's count of actions and the last applied
-action of each kind, which it keeps for the whole session, so they hold
-however many entries it dropped. The result returns the same record. When writing it fails, such as for a
-folder something else wrote into, the witness keeps its stages: check the
-stage that ended it again, with the same task, and REA writes the record
-without checking again. Once it is saved, the same check returns the saved
-record again, so a record saved as its call was cancelled is not lost. A
-computer is witnessed once; witness again from a fresh computer.
-
-See the [specification](specs/desktop-app-environments/build-witness/spec.md)
-for scope and verification.
@@ -1,82 +0,0 @@
-# Documentation ownership and authoring
-
-Use the [documentation directory](../README.md) to find existing material before
-adding another guide. Preserve one canonical owner for each contract or workflow;
-link to that owner instead of copying its claims into several guides.
-
-## Choose a destination
-
-| Document                                                 | Destination                            |
-| -------------------------------------------------------- | -------------------------------------- |
-| Installation, client setup and first CLI/MCP steps       | `docs/getting-started/`                |
-| Analyst workflows and evidence interpretation            | `docs/guides/<domain>/`                |
-| Analysis-engine configuration and format prerequisites   | `docs/providers/`                      |
-| Shared runtime contracts and evidence semantics          | `docs/reference/`                      |
-| Development, testing, release and authoring instructions | `docs/development/`                    |
-| Composition diagrams                                     | `docs/architecture/`                   |
-| Compatibility changes for a released version             | `docs/migrations/`                     |
-| One feature specification, plan and tasks                | `docs/specs/<domain>/<feature-slug>/`  |
-| One architectural decision                               | `docs/adr/<domain>/<decision-slug>.md` |
-
-Use meaningful, lowercase domain and feature slugs. Global numeric prefixes are
-unnecessary: different domains can add features independently, and branches do
-not compete for the next sequence number. Check the existing domain directory
-and linked issues before creating a feature with the same slug.
-
-Guides describe existing behavior and limitations. Specs define one proposed
-feature or domain change; an existing guide does not become a specification by
-moving it into `specs/`.
-
-## Feature lifecycle
-
-Create the specification before implementation. Each feature directory contains:
-
- `spec.md`: problem, desired behavior, requirements, acceptance and non-goals.
- `plan.md`: the single implementation plan, contracts and architectural choices.
- `tasks.md`: incremental, testable steps linked to requirements and verification.
-
-Split independent domains or separately reviewable features before writing their
-specs. A broad `ROADMAP.md`, when useful, only lists child specifications, order
-and dependencies; requirements and implementation tasks belong to each child.
-Cross-repository contracts have one producer-owned specification. Consumers link
-to that contract instead of maintaining competing copies.
-
-Record an isolated architectural decision separately in
-`docs/adr/<domain>/<decision-slug>.md`, with **Status**, **Context**,
-**Decision** and **Consequences**. Link the ADR from affected specifications.
-Do not create decision records for routine file moves or invent past decisions.
-
-Specs do not replace the contribution-scope decision required for a new provider
-or expanded execution authority. Follow
-[contribution scope](https://github.com/morluto/rea/blob/main/CONTRIBUTING.md#contribution-scope).
-
-## Links and public routes
-
-Use relative links to physical Markdown files so GitHub readers can follow them.
-Link repository files outside `docs/` with their full GitHub URLs. Preserve
-existing heading anchors when moving a guide.
-
-[`documentation.ts`](https://github.com/morluto/rea/blob/main/docs/.vitepress/documentation.ts)
-owns categorized site navigation and the existing guides' stable public routes.
-Update it when adding or moving a guide. VitePress rewrites categorized sources
-to the existing public paths; its Markdown hook resolves repository links from
-the physical source and renders them against those public routes. Keep basenames
-and route assignments unique. Edit links use the physical source file.
-
-For a move, search for both the basename and its old full path. Update README
-translations, authored skills, verification instructions, documentation-fact
-readers and release configuration when they consume that path. Preserve
-historical release records and references bound to earlier commits or tags.
-
-## Generated ownership and checks
-
-The [documentation directory](../README.md#machine-owned-documentation) identifies
-the machine-owned outputs and their producers. Their existing paths are retained
-because scripts, package consumers and release history depend on them. Change
-canonical sources and regenerate; do not fix a generated projection by hand.
-
-Run `npm run docs:check` for documentation facts and generated consistency, and
-`npm run verify:docs:routes` to build the complete production site and check local
-links, anchors and physical edit targets.
-When a physical path moves, also run the tests that read it. Follow
-[development checks](testing.md#developer-commands) before requesting review.
@@ -6,7 +6,7 @@ Disconnecting the inspection's page session can clear caller-owned
 `navigator.platform` emulation inside Chromium. REA cannot restore another
 client's complete user-agent/client-hint configuration. Use a disposable target
 or let the owning client reapply its configuration; see the shared
-[CDP state limitation](../web/browser-observation.md#provider-authorities).
+[CDP state limitation](browser-observation.md#provider-authorities).

 This passive runtime surface is distinct from the target-free static
 [`analyze_javascript_application`](javascript-artifact-reconstruction.md)
@@ -14,7 +14,7 @@ workflow. Static analysis reads a local ASAR or extracted directory without
 executing application code. Passive observation inspects an existing Electron
 page. The results keep static inferences and runtime observations distinct.
 Packaged fuse state is a separate static read:
-[`inspect_electron_fuses`](../../electron-fuses.md) reports whether this binary will
+[`inspect_electron_fuses`](electron-fuses.md) reports whether this binary will
 honor Inspector flags, `ELECTRON_RUN_AS_NODE`, embedded ASAR integrity, and
 `app.asar`-only loading.
 Use the separate
@@ -328,7 +328,7 @@ budget used by static ASAR reads: 16 MiB / 16777216 bytes by default, seeded by
 `update_analysis_settings` can override `asar.max_header_bytes` for new
 operations without restarting REA. Cached headers are checked against each
 operation's admission, including after a decrease. See the
-[settings design](../../design/limits-and-recovery.md#failure-and-retry).
+[settings design](design/limits-and-recovery.md#failure-and-retry).
 An oversized header is
 not parsed; selecting a member path does not bypass admission, and the page
 stays unauthorized. The header cache separately retains at most that many bytes
@@ -23,7 +23,7 @@ and consider setting both `REA_MCP_INPUT_SCHEMA_PROFILE` and
 advertised output schema to 4,096 bytes by relaxing nested client validation;
 REA still validates complete results against the canonical contracts. Pair
 this with retained summaries and selected inventory views to limit the context
-needed for one question. See [MCP contracts](reference/mcp-contracts.md) for the profiles
+needed for one question. See [MCP contracts](mcp-contracts.md) for the profiles
 and their client compatibility tradeoffs.

 The layout facts follow ESP-IDF v6.1 (`esp_app_format.h`, `esp_app_desc.h`,
@@ -11,20 +11,7 @@ select a returned ELF separately for supported Ghidra analysis.

 On Linux, Binwalk and Unblob run as REA-owned processes and require a
 procps-compatible `ps` on REA's `PATH`; see the shared
-[Linux process prerequisite](../../getting-started/installation.md#linux-owned-process-prerequisite).
-
-## Compare stored firmware components
-
-For supported FIT and legacy uImage containers, use the built-in
-`inspect-artifact` / `inspect_artifact` inventory and shared
-`compare-artifacts` / `compare_artifacts` workflow. This route needs no Binwalk,
-Unblob or extraction: exact logical paths, stored-byte hashes and declared
-metadata establish component changes, with source Evidence and explicit unknowns.
-The outer container at `.` is separate from its children. See the
-[FIT version comparison recipe](../../fit-images.md#comparison) for CLI,
-MCP, summary delivery and selected supporting facts. Its real-data verification
-covers a pair of OpenWrt FIT releases; it does not establish comparison of
-decoded root filesystems or arbitrary firmware formats.
+[Linux process prerequisite](installation.md#linux-owned-process-prerequisite).

 ## Caller-supplied tools

@@ -209,7 +196,7 @@ Select a verified native child for the existing tools:

 Then use `analyze_function`, `inspect_native_api` or the other native primitives.
 Native architecture and executable validation still apply. Generic
-[MIPS ELF](../../providers/ghidra-mips.md) and [RISC-V ELF](../../providers/ghidra-riscv.md) lanes are separate
+[MIPS ELF](ghidra-mips.md) and [RISC-V ELF](ghidra-riscv.md) lanes are separate
 documents with their own admission boundaries. This milestone does
 not add PPC decompilation, raw flash load profiles, bootloader/device
 tree semantics, vulnerability scanning, emulation or hardware runtime capture.
@@ -258,12 +245,9 @@ tree semantics, vulnerability scanning, emulation or hardware runtime capture.
  3, allowed range 1–10.

 Staging budgets are polled and rechecked after exit; short-lived overshoot is
-possible. The per-file process limit is one byte above the larger of the selected
-payload budget and the fixed report/diagnostic file allowances, so a small payload
-selection still permits the mandatory report, and a staged file the kernel stops
-at the limit exceeds its budget instead of passing as complete. A tighter
-inherited host limit still applies and can remove that byte, so a staged file
-that reaches the installed limit is rejected as possibly truncated.
+possible. The per-file process limit is the larger of the selected payload budget
+and the fixed report/diagnostic file allowances, so a small payload selection
+still permits the mandatory report. A tighter inherited host limit still applies.
 The inherited file-size limit bounds each file, not total storage;
 address-space limits are per process, not an aggregate memory quota. Worker
 count is not CPU affinity for every external extractor. These limits do not
@@ -317,7 +301,7 @@ bootloader image, such as an OTA download or app partition, for its chip,
 classified segments, checksum and SHA-256 results, descriptor and Secure Boot
 v2 signature blocks. `extract-artifact` / `extract_artifact` writes one file
 per segment and signature block. Reading is portable and needs no external
-tool. See [ESP images](../../esp-image.md).
+tool. See [ESP images](esp-image.md).

 ## Inspect ESP flash dumps

@@ -328,11 +312,11 @@ facts for the bootloader and each app partition, and the OTA records with a
 derived selection; the running partition stays unknown. Extraction writes
 each partition, `nvs_keys` included, as an ordinary file. For a dump that
 does not start at flash address 0, select `esp-flash-image` with
-`flash_offset`. See [ESP flash images](../../esp-flash-image.md).
+`flash_offset`. See [ESP flash images](esp-flash-image.md).

 ## Inspect extracted devicetrees

-Use [`inspect_devicetree`](../../devicetree.md) / `rea inspect-devicetree` on an
+Use [`inspect_devicetree`](devicetree.md) / `rea inspect-devicetree` on an
 extracted DTB for its node/property tree, reservations, hardware summary and
 selected phandle relationships. FDT v16/v17 inspection is portable and requires
 no external tool or disassembler.
@@ -343,7 +327,7 @@ Use `inspect-artifact` / `inspect_artifact` on an Intel HEX or Motorola S-record
 file for its address regions, declared start address and record facts, then
 `extract-artifact` / `extract_artifact` for one raw file per region. Decoding is
 portable and requires no external tool. See
-[Intel HEX and S-record images](../../hex-records.md).
+[Intel HEX and S-record images](hex-records.md).

 ## Inspect U-Boot legacy uImages

@@ -356,7 +340,7 @@ is extractable as `payload.bin`, and multi-file and script images additionally
 expose each sub-image as `image-<n>.bin` from the stored size table. Declared
 addresses are facts from the header, not proven entry points, and compressed
 payloads stay as stored. Intel HEX/S-record and FIT images are separate
-readers and are not covered here. See [U-Boot legacy uImage](../../uimage.md) for
+readers and are not covered here. See [U-Boot legacy uImage](uimage.md) for
 component padding, preserved names, resource policies and verification scope.

 ## Inspect UF2 and DfuSe images
@@ -366,7 +350,7 @@ address regions and its block numbering, or on a DfuSe file for its targets,
 elements and DFU suffix, then `extract-artifact` / `extract_artifact` for one
 raw file per region or element. A DfuSe suffix CRC mismatch follows
 `integrity_policy`. Decoding is portable and requires no external tool. See
-[UF2 and DfuSe images](../../uf2-dfuse.md).
+[UF2 and DfuSe images](uf2-dfuse.md).

 ## Inspect U-Boot FIT images

@@ -374,4 +358,4 @@ Use `inspect-artifact` / `inspect_artifact` on a U-Boot FIT (`.itb`) for its
 images, declared load and entry addresses, configurations and verified hashes,
 then `extract-artifact` / `extract_artifact` for one raw file per image.
 Decoding is portable and requires no external tool. See
-[U-Boot FIT images](../../fit-images.md).
+[U-Boot FIT images](fit-images.md).
@@ -149,116 +149,10 @@ After extraction:

 ## Comparison

-Use the shared `compare-artifacts` / `compare_artifacts` workflow for exact
-component paths and stored content identities. Neither extraction nor an external
-firmware engine is required. This compares the bytes exposed by this FIT reader;
-it does not inspect files inside a compressed root filesystem, match renamed
-components, or establish runtime equivalence.
-
-### CLI
-
-Retain each complete inspection while returning a summary:
-
-```sh
-rea inspect-artifact /absolute/baseline.itb --detail summary \
-  --evidence_output /absolute/baseline-evidence.json --json
-rea inspect-artifact /absolute/candidate.itb --detail summary \
-  --evidence_output /absolute/candidate-evidence.json --json
-```
-
-The CLI returns a `{summary, evidence_bundle}` receipt. Use each response's
-`summary.normalized_result.parent_evidence_id` as the corresponding
-`evidence_id` below. Save this request as `comparison.json`, replacing the paths
-and IDs with the returned values, then run `rea compare-artifacts comparison.json
--json`. Evidence-file paths must be absolute. Naming the exact complete parent
-avoids ambiguity when a bundle contains several inspection or inventory records.
-
-```json
-{
-  "left": {
-    "kind": "evidence-file",
-    "path": "/absolute/baseline-evidence.json",
-    "evidence_id": "COMPLETE_BASELINE_EVIDENCE_ID"
-  },
-  "right": {
-    "kind": "evidence-file",
-    "path": "/absolute/candidate-evidence.json",
-    "evidence_id": "COMPLETE_CANDIDATE_EVIDENCE_ID"
-  }
-}
-```
-
-### MCP
-
-For each file, call `open_binary` with its path, then `inspect_artifact` with
-`{"detail":"summary"}`. Opening the second file retains the first inspection's
-Evidence. Compare the two complete parent IDs without resending their graphs:
-
-```json
-{
-  "name": "compare_artifacts",
-  "arguments": {
-    "left": {
-      "kind": "retained-evidence",
-      "evidence_id": "COMPLETE_BASELINE_EVIDENCE_ID"
-    },
-    "right": {
-      "kind": "retained-evidence",
-      "evidence_id": "COMPLETE_CANDIDATE_EVIDENCE_ID"
-    }
-  }
-}
-```
-
-The result counts unchanged, added, removed, changed, unknown and contradictory
-paths, returning every delta inline with source Evidence links. The root `.` is
-the outer FIT and is counted separately from `images/<unit-name>.bin`. A changed
-outer hash therefore does not imply every component changed. Additions and
-removals require complete container-entry coverage; ambiguous duplicate paths or
-missing observations cannot prove absence or equivalence.
-
-Artifact comparison includes an image's payload interpretation, including load
-and entry declarations. Equivalent external offset forms and inventory positions
-leave those declarations unchanged. Unavailable interpretations remain unknown,
-while independently known changes survive; a changed row with an `availability`
-dimension does not establish the unavailable field's value.
-
-For supporting facts, batch selected paths rather than requesting the entire
-inspection again:
-
-```json
-{
-  "name": "inspect_analysis_view",
-  "arguments": {
-    "source": {
-      "kind": "retained-evidence",
-      "evidence_id": "COMPLETE_BASELINE_EVIDENCE_ID"
-    },
-    "view": {
-      "kind": "inventory",
-      "collection": "occurrences",
-      "logical_paths": ["images/kernel-1.bin", "images/fdt-1.bin"],
-      "fields": [
-        "artifact_id",
-        "logical_path",
-        "hash_status",
-        "source_location",
-        "source_path"
-      ],
-      "offset": 0,
-      "limit": 64
-    }
-  }
-}
-```
-
-Read `collection: "nodes"` with those `artifact_ids` and `fields: ["sha256",
-"size"]` to obtain content facts. Join by `artifact_id`, not array position.
-Continue using the returned page metadata when necessary. Source locations are
-ranges in the original FIT, not decoded filesystem offsets. Complete Evidence
-remains available through the retained parent and `export_evidence_bundle`.
-Summary and field selection reduce delivery only; they do not skip inventory
-hashing or change coverage.
+Artifact comparison reports changes to an image's payload interpretation,
+including load and entry declarations. Equivalent external offset forms and
+inventory positions leave those declarations unchanged. Unavailable
+interpretations remain unknown, while independently known changes survive.

 ## Verification

@@ -276,18 +170,3 @@ No image was executed.
 For small containers, complete delivery avoids an additional view request.
 Choose summary and selected views when the omitted facts justify that extra
 request; summary delivery does not reduce the underlying inventory work.
-
-The component comparison workflow was additionally checked on the official
-[OpenWrt 24.10.0](https://downloads.openwrt.org/releases/24.10.0/targets/mediatek/filogic/)
-and [24.10.1](https://downloads.openwrt.org/releases/24.10.1/targets/mediatek/filogic/)
-`abt_asr3000-initramfs-recovery.itb` images (8,519,680 and 8,585,216 bytes).
-Their SHA-256 values are
-`083b174e81ed373f2d2f2ea5366f9291767d95375383528fd6b9955ad815b85a` and
-`41129cce68ad6269e5c8c48ef110f97682d6c4202ff2198bfd0d300c3dac132a`.
-An independent FDT byte-range/hash oracle found changed kernel and initrd bytes
-and an identical DTB; REA reported those two changed components, the changed
-outer `.` and one unchanged component. A controlled copy changing only the root
-timestamp reported only `.` changed and all three components unchanged. Public
-CLI comparison of the exported source Evidence matched the MCP Evidence exactly;
-summary and selected inventory views matched the independent ranges and hashes.
-These checks did not decompress either initrd or execute the firmware.
@@ -175,9 +175,8 @@ are separate from the initialized MZ module. Headerless COM requires the
 from the filename or unrecognized bytes. DOS extenders without an admitted
 MZ real-mode entry remain outside this import boundary.

-DOS MZ is available through Ghidra, with no Hopper support claim. Windows Ghidra
-P0 admits DOS MZ read-only: function annotations and naming edits are refused
-there, and explicit COM is not admitted. macOS x64 DOS verification remains unverified.
+DOS MZ is available through Ghidra, with no Hopper support claim. It is outside
+the Windows native PE P0 boundary. macOS x64 DOS verification remains unverified.

 ## Real verification

@@ -79,7 +79,7 @@ separate ABI flags record, FP attribute values are admitted only when absent,
 recordless profile. Parsed values are retained in the MIPS analysis profile.
 A carved ELF whose section header table extends beyond the captured file is
 refused when the target is opened, before provider selection, as is every ELF
-declaration beyond EOF ([installation](../getting-started/installation.md#ghidra)). The refusal
+declaration beyond EOF ([installation](installation.md#ghidra)). The refusal
 names the declared range and the file size. It applies even when a
 program-header ABI record was captured: an uncaptured section header could
 carry an unsupported or conflicting declaration, so the captured bytes are not
@@ -8,7 +8,7 @@ labels, functions, or memory bytes. The hydration semantics are adapted from
 `effeb734fc570c32650f88b159608979dc7b423e` (MIT), cross-checked against
 .NET's `MethodTable.h` at runtime commit
 `a3b2d40328be0be3f8dd43f0e5cc925b8827b044` (MIT). The required notice ships in
-[`licenses/nativeaot-parser-MIT.txt`](https://github.com/morluto/rea/blob/main/licenses/nativeaot-parser-MIT.txt).
+[`licenses/nativeaot-parser-MIT.txt`](../licenses/nativeaot-parser-MIT.txt).

 The optional headless Ghidra adapter remains available for database annotations
 and broader recovery. It uses the same pinned upstream commit as an opt-in
@@ -158,7 +158,7 @@ does not imply that ordinary native disassembly/decompilation is impossible.

 ## Verification

-See [the dedicated lane](../development/testing.md#optional-nativeaot-ghidra-analysis).
+See [the dedicated lane](testing.md#optional-nativeaot-ghidra-analysis).
 Fixtures are source-built benign .NET programs with inheritance, an interface,
 virtual dispatch, representative arithmetic and frozen strings. Independent
 compiler/linker symbols and raw directory bytes provide the oracle. Stripped
@@ -2,28 +2,19 @@

 REA imports one target into an ephemeral Ghidra database. Linux/macOS support
 read-only analysis and atomic function-name/entry-comment edits; Windows P0 is
-read-only. GUI controls and writes to caller-selected source databases are unavailable.
+read-only. GUI controls and persistent database mutation are unavailable.
 Executable bytes remain unchanged.

-An opt-in [owned Program checkpoint](../getting-started/installation.md#automatically-checkpoint-an-owned-ghidra-program)
-retains analysis across Linux/macOS processes. It saves initial completed analysis
-and normal-close metadata changes to `REA_GHIDRA_CHECKPOINT_DIR`; cancellation
-and process failure recover only the last successfully saved state. The restored
-packed Program's digest is reported with restored observations. Initial analysis
-keeps one stable generation through its first save; later saved states bind their
-content digest in profile identity. Restoration does not turn prior
-database state into a fresh discovery. The default remains ephemeral.
-
-Use [installation](../getting-started/installation.md#ghidra) for supported hosts, prerequisites,
+Use [installation](installation.md#ghidra) for supported hosts, prerequisites,
 configuration, startup deadlines, resource controls, and cleanup recovery.
-[Linux Ghidra launches](../getting-started/installation.md#linux-owned-process-prerequisite) also
+[Linux Ghidra launches](installation.md#linux-owned-process-prerequisite) also
 require a procps-compatible `ps` on REA's `PATH` for process ownership checks.
 [Windows P0](windows-ghidra-p0.md) has its own admission and lifecycle boundary;
 [NativeAOT observations](ghidra-nativeaot.md) include a built-in read-only PE
 snapshot parser and a separate optional annotation extension. Check the
-[release boundary](../getting-started/installation.md#released-package-and-main) when using npm.
+[release boundary](installation.md#released-package-and-main) when using npm.

-See [import language and analysis seeds](../getting-started/installation.md#ghidra-import-language-and-analysis-seeds)
+See [import language and analysis seeds](installation.md#ghidra-import-language-and-analysis-seeds)
 to override the header-detected language or seed analysis. An override that conflicts with a fixed raw, DOS, PSP, MIPS, RISC-V or GameCube DOL import
 is a configuration error naming the conflicting settings. It does not make an
 otherwise admitted target unsupported; REA preserves the requested settings.
@@ -52,7 +43,7 @@ not clear it or alter session readiness. Log paths refer to the owned ephemeral
 runtime and are removed by normal cleanup.

 Provider selection and profile identity follow
-[MCP contracts](../reference/mcp-contracts.md#identity-and-discovery). One deep
+[MCP contracts](mcp-contracts.md#identity-and-discovery). One deep
 provider stays bound to the target; runtime failure never selects another
 provider automatically. The contracts below describe Ghidra observations,
 not equivalence with another engine's pseudocode or analysis database.
@@ -89,13 +80,6 @@ does not prove text is absent. Both list and search Evidence carry this
 limitation. When an address is known, use `read_bytes` and `xrefs` to inspect
 bytes and references.

-String searches and `trace_feature` retain each matched row's Ghidra-reported
-encoding, termination and byte length. These describe the database's defined
-data, not independent proof of the original source encoding. Procedure searches
-and trace matches likewise retain Ghidra's external and thunk classification.
-The Ghidra analysis profile identifies this search projection, so older
-snapshots with unqualified search rows cannot replay under the new profile.
-
 ## PE debug-symbol coverage

 The post-analysis handshake reports Ghidra's PDB Program Information attributes:
@@ -140,11 +124,6 @@ also accept source-file byte offsets. Existing symbols and analysis addresses
 take precedence; a `0x`-prefixed number that resolves to no procedure falls back
 to its observed source mapping. Use `--file-offset=0x...` on the CLI or
 `procedure: "file-offset:0x..."` through MCP to select file coordinates explicitly.
-To select an analysis address without the bare-hex fallback, qualify it with its
-Ghidra address space, for example `ram:0x...`. The `inspect-native-load-image`
-CLI command or MCP `inspect_native_load_image` reports Ghidra's observed default
-address space; use the space appropriate to the address, and retain any
-load-image verification limitations.
 Multiple mapping candidates fail as ambiguous rather than selecting a bank or
 address space. A successful conversion retains the file offset, mapped address
 and procedure entry in raw Evidence and `locations`.
@@ -276,21 +255,9 @@ Runtime updates apply to newly accepted operations on the existing Program.
 They preserve accepted budgets and do not clear cleanup blockers or change the
 client deadline. Transient decompile timeout failures remain uncached so the
 same function can be retried after raising the limit. See the
-[settings design](../design/limits-and-recovery.md) for snapshots, precedence,
+[settings design](design/limits-and-recovery.md) for snapshots, precedence,
 and provider integration.

-When `inspect_native_instruction` selects a byte inside a listed instruction,
-`containing_instruction` reports its separate start, length and Ghidra Listing
-text, retaining any non-default address space. The requested address remains
-unchanged, and a containing function may be absent. For defined data, the same
-tool reports its containing object's start, length and type path; use the start
-with `inspect_native_data_type` to inspect its layout. This does not select a
-field or union member. These are listing observations, not proof of execution or
-an alternate decode. Earlier Evidence can
-omit the field. The analysis-profile revision prevents older snapshots from
-replaying results without it; open the target without the old snapshot and save
-a fresh snapshot when needed.
-
 Function extents and instruction completeness refer to Ghidra's analyzed body.
 An inferred no-return call can terminate that body before subsequent bytes.
 Pseudocode, assembly, procedure info, instruction windows, incoming and outgoing
@@ -363,11 +330,9 @@ Without bounds, loaded memory blocks are eligible, in Ghidra address order.
 Blocks that are not loaded (file parts such as `.symtab`) and overlay blocks are
 listed in `searched.skipped_not_loaded` and are not searched; pass `start` or
 `end` in their address space to search them.
-Overlapping matches are included, including across adjacent eligible initialized
-blocks in the same address space. Gaps and excluded or uninitialized blocks break
-a search run. Each match reports its address, starting segment, unique source file
-offset for that starting address (or null), and containing procedure (or null).
-A starting offset does not imply the full match is contiguous in the file.
+Overlapping matches are included; matches never cross block boundaries.
+Each match reports its address, segment, unique source file offset (or null),
+and containing procedure (or null).

 Pages default to 100 matches and accept 1 to 1000. Pass `next_cursor` as `cursor`
 with the same target, profile, pattern, mask and bounds to continue. `complete`
@@ -93,15 +93,8 @@ The maintained PSP fixture builds from `tests/conformance/psp/`, never executes,
 and is independent of commercial game data. PSP GNU tools supply ELF/ABI,
 raw ABI-record, symbol and encoding observations; REA's parsed target and saved
 snapshot must agree with the independent ABI declaration. Public CLI/MCP must
-recover known functions, a direct call, the immediate `0x1234`, BITREV, a
-global word and a marker. The additional source-owned VFPU function contains
-`vpfxs`, `vpfxt`, `vpfxd` and three `vadd.q` instructions.
-The PSP lane checks their fixed encoded bytes and Ghidra's decoded mnemonics
-through `inspect_native_instruction`; an analyzed dossier reports available
-high-p-code opaque-operation and truncation observations. Neither decoded
-instructions nor `CALLOTHER` counts establish prefix consumption, lane-level
-arithmetic or emulator/hardware equivalence.
-The verifier
+recover known functions, a direct
+call, the immediate `0x1234`, BITREV, a global word and a marker. The verifier
 checks observed loader/language, original bytes, Evidence, snapshot reopening,
 and an A-B-A target switch with different global contents at the same address.
 A snapshot for A must not open B. Cleanup must finish before success is reported.
@@ -265,7 +265,7 @@ definitions use it.
 Ghidra 12.1.4 PUBLIC with a 64-bit JDK 21+ is required, and on macOS the release
 tree ships no host decompiler binary, so `Decompiler/os/<platform>/decompile` and
 `sleigh` must come from your own build; see
-[installation](../getting-started/installation.md#ghidra).
+[installation](installation.md#ghidra).

 Run `npm run verify:ghidra:riscv` with an existing Ghidra 12.1.4 installation,
 JDK 21+, and a RISC-V-capable Clang, LLD, LLVM readelf and LLVM objdump. The
@@ -196,7 +196,7 @@ the same virtual alignment are searched once; partially overlapping spans
 consume the cumulative search budget
 and fail with a CPU resource constraint when it is exhausted. Oversized results
 fail without partial success. MCP also applies
-its [response transport budget](../../reference/mcp-contracts.md), which counts both text and
+its [response transport budget](mcp-contracts.md), which counts both text and
 structured content; a report within the metadata limit can still require export
 from retained Evidence. These limits are not operating-system memory or CPU
 isolation.
@@ -25,33 +25,6 @@ by default; `--integrity-policy record-and-continue` retains the observed bytes
 and an explicit untrusted contradiction. An all-zero MD5 is an unknown claim,
 not a verified digest.

-Artifact comparison pairs members by `logical_path`, the stored path without
-`res://`, and compares their bytes and occurrence facts. It does not compare
-`godot-pck-entry` metadata. Godot 4.3
-[stores `res://` paths](https://github.com/godotengine/godot/blob/77dcf97d82cbfe4e4615475fa52ca03da645dbd8/editor/export/editor_export_platform.cpp#L228)
-and [keys members by them](https://github.com/godotengine/godot/blob/77dcf97d82cbfe4e4615475fa52ca03da645dbd8/core/io/file_access_pack.cpp#L50-L52).
-Godot 4.4.1
-[stores paths without the prefix](https://github.com/godotengine/godot/blob/49a5bc7b616bd04689a2c89e89bda41f50241464/editor/export/editor_export_platform.cpp#L257-L260)
-and [removes it before keying](https://github.com/godotengine/godot/blob/49a5bc7b616bd04689a2c89e89bda41f50241464/core/io/file_access_pack.cpp#L48-L50).
-Each version finds `res://scenes/main.gd` in its own export, but comparing the
-stored `source_path` would mark every member changed between such exports.
-`logical_path` names the member Godot's lookup finds, except in two cases.
-REA normalizes Unicode to NFC, so a member renamed only between Unicode forms
-compares unchanged, although Godot treats it as another path. Godot reads `\`
-as `/` and REA keeps it literal, so a member spelled with backslashes compares
-as removed and added. Directory order and offsets are layout. The encryption
-bit, the only member flag REA admits, is the occurrence's `encrypted` field. A
-member whose encryption changes compares `unknown` in `metadata` and
-`availability`: the change is known, but REA does not read encrypted bytes,
-so whether the script changed is unknown. Godot's exporter
-[stores the MD5 of a member's original bytes](https://github.com/godotengine/godot/blob/a13da4feb8d8aefc283c3763d33a2f170a18d541/editor/export/editor_export_platform.cpp#L465-L468),
-as the 4.3 and 4.4.1 exporters do, so the declared MD5 does not depend on the
-encryption IV. Encrypted members whose declared MD5s differ therefore also
-compare `unknown` in `metadata` and `availability`: the MD5s declare
-different scripts, but REA cannot verify them, and equal MD5s add nothing for
-the same reason. An encrypted member with an MD5 on only one side stays
-`unknown`.
-
 ## CLI

 Start with a compact summary and keep the complete Evidence bundle:
@@ -36,8 +36,6 @@ The MCP tool `project_harmony_application_graph` takes the same

 - exact component paths, artifact IDs, and hashes (manifests, Ark bytecode,
  resources, native libraries, JavaScript, signing)
- `unclassified_components` with the same paths and content identities for
-  authenticated files outside those categories and the App Pack child list
 - a packaging-model hint: Stage is claimed only from an exactly cased `module.json` entry
  outside a classified resource path, FA only from `config.json` outside a
  classified resource path, otherwise `unknown`
@@ -57,24 +55,6 @@ being classified as code files. Ark and JavaScript runtime hints summarize the
 classified bytecode and JavaScript lists; supported source extensions share the
 same classification rule as their component rows.

-`unclassified_components` preserves files such as `pkgContextInfo.json`,
-`.pages.info`, a HarmonyOS `.har` shared library, and a non-certificate
-`META-INF` entry without interpreting their contents. The `.har` suffix also
-names HTTP Archive JSON, so identifying one needs verified ZIP bytes rather than
-a path rule. Different paths sharing the same bytes remain separate entries. App
-Pack children of an App Pack root are already reported in `app_pack_children`,
-so they are not repeated as unclassified files. A nested `.hap` or `.hsp` member
-of a HAP or HSP root is disclosed in `unclassified_components` instead, because
-child-package inventory is not recursive. Unreadable or encrypted content remains
-in `unavailable_components` with unknown identity instead.
-
-`coverage.status: "complete-within-inventory"` describes the authenticated
-source inventory and bounded bridge projection, not semantic understanding of
-every file. Unclassified files do not make a complete inventory partial; missing
-inventory pages, source coverage limits, unavailable content and bridge limits
-still qualify coverage independently. An empty unclassified list on a partial
-inventory does not establish that the whole package has no unclassified files.
-
 Every claim is path-presence only. Manifest semantics (module identity,
 abilities, entry points, permissions, dependencies), Ark bytecode contents and
 versions, resource resolution, signing verification, and observed native
@@ -82,12 +62,6 @@ boundaries are out of scope for this increment and stay in the projection's
 `limitations` array until a dedicated HarmonyOS provider exists. REA fails
 closed on packages whose inventory cannot be authenticated.

-`pkgContextInfo.json` is inventoried and listed as an unclassified component but
-never read, so its `isSO` declarations do not narrow `bridge_candidates`. When
-that entry is present the projection adds a limitation naming the unread
-declaration, so a path-convention hypothesis is not mistaken for a package
-declaration.
-
 ## Verification lane

 `npm run fixtures:harmony` downloads the SHA-256-pinned 1.0.1 HAP release
@@ -36,10 +36,7 @@ regions and are never filled.

 Region `format_metadata` (`hex-record-region`) records `start_address`,
 `end_address`, `length`, `record_count`, and `first_line`/`last_line`: the
-1-based line span of the contributing data records. `compare_artifacts`
-compares none of these fields: a region's name encodes its start and end
-addresses, its length follows from them, and record and line counts are
-layout.
+1-based line span of the contributing data records.

 Root `format_metadata` (`hex-records`) records:

@@ -51,19 +51,13 @@ was established; failed registrations remain unavailable. Correct
 launch environment. Restart/reconnect that server after changing its environment;
 an export in another shell does not update a running server.

-An HTTP registration's `url` must use `http` or `https` without URL credentials,
-and its host must be `localhost`, `127.0.0.1`, `[::1]`, or the Docker/Podman
-host-gateway name `host.docker.internal` or `host.containers.internal`. Use a
-gateway name when REA runs in a container and IDA MCP listens on the container
-host. REA refuses every other host.
-
 Open the **original input binary** in REA, not an `.idb` or `.i64` database. Its SHA-256 must match IDA's recorded input hash. REA checks the attached identity and image base around each analysis request. A mismatch or target switch fails with recovery guidance. The original input must remain readable by REA; WSL can use its mounted alias while the GUI runs on Windows. Attached profiles, including native mode, refuse universal Mach-O inputs at admission: every slice shares the recorded whole-file hash, so REA cannot verify which slice the GUI loaded. Open a thin file extracted with `lipo -thin` in both IDA and REA, or use headless mode, which analyzes the selected slice.

 REA's close operation releases its MCP connection or proxy. It never saves or closes the existing GUI database. External edits remain visible because results are live and are not replayed from snapshots. These checks do not lock the GUI or prove that the database is unpatched.

 ## Optional native IDA MCP bridge

-IDA Pro and IDA Free can use the separate [ida-free-mcp native plugin](https://github.com/0xshlomil/ida-free-mcp) through an explicit attached registration. Install and start that plugin using its upstream instructions, open the original binary in the IDA GUI, and wait for analysis. The native MCP 1.1.2 release binds `0.0.0.0` without a listen-address setting. Restrict inbound access with the host firewall or use an upstream build that binds only to loopback before starting it. REA's local URL restriction does not change the plugin's listener. REA does not install IDA, build the plugin, activate a license, or launch the GUI.
+IDA Pro and IDA Free can use the separate [ida-free-mcp native plugin](https://github.com/0xshlomil/ida-free-mcp) through an explicit attached registration. Install and start that plugin using its upstream instructions, open the original binary in the IDA GUI, and wait for analysis. The native MCP 1.1.2 release binds `0.0.0.0` without a listen-address setting. Restrict inbound access with the host firewall or use an upstream build that binds only to loopback before starting it. REA's loopback URL restriction does not change the plugin's listener. REA does not install IDA, build the plugin, activate a license, or launch the GUI.

 ```json
 {
@@ -245,7 +239,7 @@ Complete body ranges, typed reference edges, CFG, referenced data, source locals

 ## Verification

-Run `npm run verify:ida -- --target /absolute/path/to/program --procedure main` with a configured upstream server. It exercises production CLI and MCP tools, validates their output contracts and Evidence, checks original-input preservation and session cleanup, and keeps local target data out of its console summary. Supply `--package-root` to verify an extracted or installed package. See [testing](../development/testing.md) for the distinction between adapter tests and real-provider evidence.
+Run `npm run verify:ida -- --target /absolute/path/to/program --procedure main` with a configured upstream server. It exercises production CLI and MCP tools, validates their output contracts and Evidence, checks original-input preservation and session cleanup, and keeps local target data out of its console summary. Supply `--package-root` to verify an extracted or installed package. See [testing](testing.md) for the distinction between adapter tests and real-provider evidence.

 Native verification requires `--second-procedure other_function --second-marker unique_second_body_text`; these options remain optional for the other profiles. The marker must occur in the second function's pseudocode and be absent from the first; the verifier also checks that returning to the first restores its text.

@@ -148,7 +148,7 @@ rea inspect-analysis-view /tmp/metadata-query.json --json
 ```

 Use the exported Evidence with the CLI's inline Evidence source format described
-in [CLI and Evidence](getting-started/cli.md#run-a-command). Compact delivery requires
+in [CLI and Evidence](cli.md#run-a-command). Compact delivery requires
 `--evidence_output`; existing files are never overwritten. The full export
 preserves every decoded row for subsequent queries without the original file.

@@ -482,7 +482,7 @@ Native address queries batch exact 64-bit hexadecimal `addresses` and `states` (
 ## Ghidra function names

 The CLI can turn a linked report into a
-[`REA_GHIDRA_SEED_FILE`](getting-started/installation.md) so Ghidra names every IL2CPP method
+[`REA_GHIDRA_SEED_FILE`](installation.md) so Ghidra names every IL2CPP method
 before auto-analysis:

 ```bash
@@ -553,7 +553,7 @@ report to 64 MiB, checking row counts before allocation and JSON/UTF-8/base64 ex
 decoding, before serialization. Names and identical literal spans are decoded
 once within one stable file snapshot; no filesystem results are cached across
 inspections. Ownership assignment also yields to cancellation. MCP also applies its
-[response transport budget](reference/mcp-contracts.md); a complete report within the
+[response transport budget](mcp-contracts.md); a complete report within the
 report limit can still require the summary and paging path.

 ## Outside this tool
@@ -566,8 +566,8 @@ report limit can still require the summary and paging path.
 - Full method signatures beyond the rendered field, parameter and return type
  names, and type names for metadata version 27.
 - Running Ghidra or another disassembler. `--ghidra-seeds` only writes a seed
-  file for [`REA_GHIDRA_SEED_FILE`](getting-started/installation.md); use the
-  [native workflow](guides/native/native-investigation.md) for native code.
+  file for [`REA_GHIDRA_SEED_FILE`](installation.md); use the
+  [native workflow](native-investigation.md) for native code.
 - Metadata versions other than 24, 27, 29, 31 and 39.

 Names come from the metadata file only. They do not establish which methods
@@ -41,33 +41,31 @@ For a first result from an extracted JavaScript application or ASAR:
 npx -y rea-agents@latest analyze-javascript-application /absolute/path/to/app --json
 ```

-See [installation and setup](getting-started/installation.md) for requirements and configuration.
+See [installation and setup](./installation.md) for requirements and configuration.

-For runtime instrumentation, see the [Frida guide](guides/runtime/frida-instrumentation.md).
+For runtime instrumentation, see the [Frida guide](./frida-instrumentation.md).

 ## Choose a guide

-The [documentation directory](README.md) lists every guide by domain.
+| Task                                                | Guides                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
+| --------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| Identify a desktop installation                     | [Runtime candidates, evidence and follow-up files](desktop-applications.md)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
+| Inspect native functions, references, or types      | [Native binaries](native-investigation.md), [Go metadata](go-binaries.md), [Rust dependencies](rust-binaries.md), [CPython pyc files](python-pyc.md), [PE certificates](pe-certificates.md), [PE imports](pe-imports.md), [PE TLS/load config](pe-load-config.md), [ELF notes](elf-notes.md), [Linux kernel modules](kernel-modules.md), [Apple IPS](apple-ips.md), [Erlang BEAM](erlang-beam.md), [offline ELF layout](binary-diagnostics.md), [recorded crashes](recorded-crashes.md)                                                                               |
+| Select a native provider or import format           | [Ghidra semantics](ghidra-provider.md), [Windows](windows-ghidra-p0.md), [DOS](ghidra-dos.md), [raw bytes](raw-binary.md), [GameCube DOL](ghidra-dol.md), [MIPS](ghidra-mips.md), [PSP](ghidra-psp.md), [NativeAOT](ghidra-nativeaot.md), [IDA](ida-provider.md), [Kuna](kuna-provider.md), [JEB](jeb-analysis.md)                                                                                                                                                                                                                                                    |
+| Analyze JavaScript or Electron artifacts            | [Static analysis](javascript-artifact-reconstruction.md), [tracing and comparisons](javascript-application-workflows.md), [application graph](javascript-application-graph.md), [source recovery](javascript-recovery.md)                                                                                                                                                                                                                                                                                                                                             |
+| Compare static JavaScript with runtime observations | [Runtime attribution](javascript-runtime-observation.md), [reconciliation](javascript-runtime-reconciliation.md), [Electron observation](electron-observation.md), [Electron fuses](electron-fuses.md)                                                                                                                                                                                                                                                                                                                                                                |
+| Inspect assemblies, packages, or firmware           | [Godot PCK](godot-pck.md), [UnityFS](unityfs.md), [U-Boot uImage](uimage.md), [.NET](managed-code-analysis.md), [Python packages](python-packaged-applications.md), [Android](android-analysis.md), [APK signatures](apk-signature.md), [Apktool resources](apktool-resource-analysis.md), [ADB acquisition](adb-device-analysis.md), [Apple](apple-application-analysis.md), [Harmony](harmony-analysis.md), [firmware](firmware-analysis.md), [ESP images](esp-image.md), [ESP flash images](esp-flash-image.md), [WASM](wasm-artifacts.md), [EVM](evm-bytecode.md) |
+| Observe or compare a browser scenario               | [CDP observation](browser-observation.md), [scenarios](browser-scenario-contract.md), [runtime evidence](web-runtime.md), [historical captures](web-network-captures.md)                                                                                                                                                                                                                                                                                                                                                                                              |
+| Serve recorded behavior as an agent environment     | [Agent environments](agent-environments.md)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
+| Trace captured website source                       | [Source locations](web-source-location.md), [module traces](website-module-trace.md), [script export](website-script-export.md)                                                                                                                                                                                                                                                                                                                                                                                                                                       |
+| Capture and compare a command                       | [Process capture](process-capture.md)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
+| Use CLI/MCP and retain evidence                     | [CLI](cli.md), [MCP contracts](mcp-contracts.md), [agent prompts](mcp-prompts.md), [obligation ledgers](reconstruction-obligation-ledgers.md)                                                                                                                                                                                                                                                                                                                                                                                                                         |

-| Task                                                | Guides                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
-| --------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| Identify a desktop installation                     | [Runtime candidates, evidence and follow-up files](desktop-applications.md)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
-| Inspect native functions, references, or types      | [Native binaries](guides/native/native-investigation.md), [Go metadata](guides/native/go-binaries.md), [Rust dependencies](rust-binaries.md), [CPython pyc files](python-pyc.md), [PE certificates](pe-certificates.md), [PE imports](pe-imports.md), [PE TLS/load config](pe-load-config.md), [ELF notes](elf-notes.md), [Linux kernel modules](kernel-modules.md), [Apple IPS](apple-ips.md), [Erlang BEAM](erlang-beam.md), [offline ELF layout](guides/native/binary-diagnostics.md), [recorded crashes](guides/native/recorded-crashes.md)                                                                                                                                                                                                                                                                                                                |
-| Select a native provider or import format           | [Ghidra semantics](providers/ghidra-provider.md), [Windows](providers/windows-ghidra-p0.md), [DOS](providers/ghidra-dos.md), [raw bytes](providers/raw-binary.md), [GameCube DOL](ghidra-dol.md), [MIPS](providers/ghidra-mips.md), [RISC-V](providers/ghidra-riscv.md), [PowerPC](ghidra-ppc.md), [PSP](providers/ghidra-psp.md), [NativeAOT](providers/ghidra-nativeaot.md), [IDA](providers/ida-provider.md), [Kuna](kuna-provider.md), [JEB](providers/jeb-analysis.md)                                                                                                                                                                                                                                                                                                                                                                                    |
-| Analyze JavaScript or Electron artifacts            | [Static analysis](guides/javascript/javascript-artifact-reconstruction.md), [tracing and comparisons](guides/javascript/javascript-application-workflows.md), [application graph](guides/javascript/javascript-application-graph.md), [source recovery](guides/javascript/javascript-recovery.md)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
-| Compare static JavaScript with runtime observations | [Runtime attribution](guides/javascript/javascript-runtime-observation.md), [reconciliation](guides/javascript/javascript-runtime-reconciliation.md), [Electron observation](guides/javascript/electron-observation.md), [Electron fuses](electron-fuses.md)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
-| Inspect assemblies, packages, or firmware           | [Godot PCK](godot-pck.md), [UnityFS](unityfs.md), [wxapkg](wxapkg.md), [U-Boot uImage](uimage.md), [.NET](guides/managed/managed-code-analysis.md), [Python packages](python-packaged-applications.md), [Android](guides/android/android-analysis.md), [APK signatures](apk-signature.md), [Apktool resources](guides/android/apktool-resource-analysis.md), [ADB acquisition](guides/android/adb-device-analysis.md), [Apple](guides/apple/apple-application-analysis.md), [Harmony](guides/harmony/harmony-analysis.md), [firmware](guides/firmware/firmware-analysis.md), [Device Tree](devicetree.md), [FIT images](fit-images.md), [UF2/DfuSe](uf2-dfuse.md), [Flutter](guides/android/flutter-analysis.md), [ESP images](esp-image.md), [ESP flash images](esp-flash-image.md), [WASM](guides/wasm/wasm-artifacts.md), [EVM](guides/evm/evm-bytecode.md) |
-| Observe or compare a browser scenario               | [CDP observation](guides/web/browser-observation.md), [scenarios](guides/web/browser-scenario-contract.md), [runtime evidence](guides/web/web-runtime.md), [historical captures](guides/web/web-network-captures.md)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
-| Serve recorded behavior as an agent environment     | [Agent environments](agent-environments.md)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
-| Trace captured website source                       | [Source locations](guides/web/web-source-location.md), [module traces](guides/web/website-module-trace.md), [script export](guides/web/website-script-export.md)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
-| Capture and compare a command                       | [Process capture](guides/runtime/process-capture.md)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
-| Use CLI/MCP and retain evidence                     | [CLI](getting-started/cli.md), [MCP contracts](reference/mcp-contracts.md), [agent prompts](getting-started/mcp-prompts.md), [obligation ledgers](reference/reconstruction-obligation-ledgers.md)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
-
-For development, use [testing](development/testing.md), [client verification](development/client-verification.md),
-[tool design](development/tool-design.md), [admission limits and recovery](design/limits-and-recovery.md),
-and [releasing](development/releasing.md).
-[Reconstruction readiness](development/reconstruction-readiness.md) describes a development
-conformance verifier. [The 6.2 migration](migrations/migration-6.2.md) records that release's
-compatibility changes; [the roadmap](development/roadmap.md) tracks future work.
+For development, use [testing](testing.md), [client verification](client-verification.md),
+[tool design](tool-design.md), [admission limits and recovery](design/limits-and-recovery.md),
+and [releasing](releasing.md).
+[Reconstruction readiness](reconstruction-readiness.md) describes a development
+conformance verifier. [The 6.2 migration](migration-6.2.md) records that release's
+compatibility changes; [the roadmap](roadmap.md) tracks future work.

 ![REA inspecting a native binary in Hopper](./assets/rea-hopper-analysis.png)
@@ -3,14 +3,14 @@
 Run REA, connect your selected agents, and check the tools needed for your task.
 Setup previews configuration changes and asks for approval before applying them.

-| Task                               | Section                                                                                                             |
-| ---------------------------------- | ------------------------------------------------------------------------------------------------------------------- |
-| Connect an agent                   | [Start setup](#start-setup), then [review changes](#review-setup-changes)                                           |
-| Install a Claude Code/Codex plugin | [Agent plugins and marketplaces](#agent-plugins-and-marketplaces)                                                   |
-| Diagnose one task                  | [Scoped readiness checks](#check-readiness-for-your-task)                                                           |
-| Configure an analysis engine       | [Hopper](#hopper), [Ghidra](#ghidra), the [IDA guide](../providers/ida-provider.md), or [Kuna](../kuna-provider.md) |
-| Update or remove REA               | [Maintenance](#diagnose-update-and-remove)                                                                          |
-| Resolve a client-specific problem  | [Client configuration](client-configuration.md)                                                                     |
+| Task                               | Section                                                                                             |
+| ---------------------------------- | --------------------------------------------------------------------------------------------------- |
+| Connect an agent                   | [Start setup](#start-setup), then [review changes](#review-setup-changes)                           |
+| Install a Claude Code/Codex plugin | [Agent plugins and marketplaces](#agent-plugins-and-marketplaces)                                   |
+| Diagnose one task                  | [Scoped readiness checks](#check-readiness-for-your-task)                                           |
+| Configure an analysis engine       | [Hopper](#hopper), [Ghidra](#ghidra), the [IDA guide](ida-provider.md), or [Kuna](kuna-provider.md) |
+| Update or remove REA               | [Maintenance](#diagnose-update-and-remove)                                                          |
+| Resolve a client-specific problem  | [Client configuration](client-configuration.md)                                                     |

 ## Start setup

@@ -374,16 +374,16 @@ choosing an operation; it works before a target is opened, and
 `result.tool_availability` reports per-operation availability, reasons and
 client requirements for the current session state. It does not guarantee that
 a particular caller-supplied input will be valid. See
-[MCP discovery](../reference/mcp-contracts.md#identity-and-discovery).
+[MCP discovery](mcp-contracts.md#identity-and-discovery).

 Select the part you want to check:

-| Task                                | Readiness check                                                            |
-| ----------------------------------- | -------------------------------------------------------------------------- |
-| Static JavaScript/Electron analysis | Run `rea analyze-javascript-application PATH --json` directly.             |
-| One analysis engine                 | `rea doctor --provider ghidra --json` (or `hopper`, `ida`, `jadx`, `kuna`) |
-| One agent registration              | `rea doctor --client codex --json` (see [client IDs](#supported-agents))   |
-| Installed workflow instructions     | `rea doctor --skill --json`                                                |
+| Task                                | Readiness check                                                          |
+| ----------------------------------- | ------------------------------------------------------------------------ |
+| Static JavaScript/Electron analysis | Run `rea analyze-javascript-application PATH --json` directly.           |
+| One analysis engine                 | `rea doctor --provider ghidra --json` (or `hopper`, `ida`, `kuna`)       |
+| One agent registration              | `rea doctor --client codex --json` (see [client IDs](#supported-agents)) |
+| Installed workflow instructions     | `rea doctor --skill --json`                                              |

 A scoped report has `scope.mode: "explicit"`. Its `scope_checks` determine
 `healthy` and the exit status. Other checks appear in `informational_checks`;
@@ -636,7 +636,6 @@ hosted connector; see [its configuration](client-configuration.md#other-client-s
 | Claude Desktop     | `claude_desktop` |
 | Codex              | `codex`          |
 | Cursor             | `cursor`         |
-| CodeBuddy          | `codebuddy`      |
 | Gemini CLI         | `gemini_cli`     |
 | Windsurf           | `windsurf`       |
 | Devin              | `devin`          |
@@ -655,7 +654,6 @@ hosted connector; see [its configuration](client-configuration.md#other-client-s
 | Factory Droid      | `droid`          |
 | Trae               | `trae`           |
 | WorkBuddy          | `workbuddy`      |
-| LM Studio          | `lm_studio`      |
 | ZCode              | `zcode`          |
 | DeepSeek Harness   | `dsh`            |
 | FreeBuff           | `freebuff`       |
@@ -665,8 +663,6 @@ hosted connector; see [its configuration](client-configuration.md#other-client-s
 `freebuff` requires `[email protected]` or later. Older releases reject
 `rea setup --client freebuff` as an unsupported client.

-`lm_studio` requires a release after 6.8.0.
-
 See [client configuration and troubleshooting](client-configuration.md) for
 configuration paths, profiles, trust policies, and schema-limit workarounds.

@@ -674,12 +670,6 @@ configuration paths, profiles, trust policies, and schema-limit workarounds.

 See [the Cordis patch and launcher setup](client-configuration.md#deepseek-harness).

-### llama.cpp
-
-llama-server can launch REA through its native stdio MCP configuration. This is
-a manual connection, not an automatic setup client ID. See the
-[local model setup](client-configuration.md#llamacpp).
-
 ### Other client settings

 See [OpenCode, Grok Build, and Grok Bot settings](client-configuration.md#other-client-settings).
@@ -698,7 +688,7 @@ Linux architectures; configure [Ghidra](#ghidra) there instead. REA itself runs
 Linux distribution with a recognized apt, dnf, or pacman package family, where
 an existing Hopper launcher is selected through `HOPPER_LAUNCHER_PATH`. Ghidra
 and IDA have their own provider-specific host requirements; Windows Ghidra uses
-the [experimental P0 boundary](../providers/windows-ghidra-p0.md).
+the [experimental P0 boundary](windows-ghidra-p0.md).

 Bazzite uses RPM packages, but REA does not install Hopper automatically on it.
 Setup skips the Hopper offer because Bazzite is outside the supported host list,
@@ -727,11 +717,6 @@ and status when publisher verification cannot download the current package.
 Hopper metadata and package downloads require HTTPS throughout the redirect
 chain; a redirect to HTTP or to a URL carrying credentials is refused before
 that destination is requested, and those credentials are not reported.
-A package download fails when no bytes arrive for 30 seconds or when it has not
-finished within 15 minutes, so a slow connection that keeps delivering bytes can
-complete. Release metadata and the publisher key keep a 10-second limit. A
-`timeout` failure reports the `limit` it reached (`stalled` or `deadline`), its
-`timeoutMs` and the `receivedBytes` before it stopped.

 On macOS, approved setup downloads the official DMG, checks its published size
 and digest, validates the application bundle, and atomically installs it to
@@ -1025,7 +1010,7 @@ output-stream closure; `output_closed: false` keeps that uncertainty explicit.
 Later requests retain the known exit instead of reducing it to socket loss.
 An external GUI's helper exit does not establish that the GUI itself exited.
 For cursor navigation, string decoding, symbol-name limits, and regex matching,
-see [Hopper analysis behavior](../guides/native/native-investigation.md#hopper-analysis-behavior).
+see [Hopper analysis behavior](native-investigation.md#hopper-analysis-behavior).

 Closing or switching a target closes its bound Hopper document, shuts down REA's
 bridge and removes its temporary socket directory. The macOS Hopper application
@@ -1149,14 +1134,13 @@ and `set_addresses_names` name a function entry or any other mapped address
 session metadata edits leave executable bytes unchanged and are discarded on close. GUI controls
 require Hopper; Windows P0 remains read-only.

-Windows P0 admits native x86, x86-64, ARMNT (Thumb-2) and ARM64 PE applications and DLLs,
-[DOS MZ executables](../providers/ghidra-dos.md), plus explicitly
-selected [raw NMOS 6502 images](../providers/raw-binary.md#nmos-6502) with a caller-supplied
+Windows P0 admits native x86, x86-64, ARMNT (Thumb-2) and ARM64 PE applications and DLLs, plus explicitly
+selected [raw NMOS 6502 images](raw-binary.md#nmos-6502) with a caller-supplied
 entry at file offset 0, on fixed local NTFS volumes. Other raw CPU families remain
 unsupported on Windows.
 The npm package bundles native Job Object ownership, protected private runtime
 DACLs, and handle-based path admission; no separate addon installation is needed.
-See the [Windows Ghidra P0 guide](../providers/windows-ghidra-p0.md) for verified scope and
+See the [Windows Ghidra P0 guide](windows-ghidra-p0.md) for verified scope and
 limitations.

 Extract Ghidra and install the JDK outside REA, then export absolute paths:
@@ -1176,11 +1160,7 @@ selected formula's `libexec/openjdk.jdk/Contents/Home`, for example
 Java version bounds declared by your Ghidra installation; REA does not select
 another JDK when `JAVA_HOME` is explicit or the PATH JVM runs. On macOS,
 when the PATH launcher cannot start a JVM, it tries executable Homebrew
-`opt/openjdk` and installed `opt/openjdk@<major>` candidates, preferring the host
-architecture's prefix and the unversioned formula within each prefix. Versioned
-aliases are considered in ascending major order within Ghidra's declared Java
-bounds; the selected executable still undergoes the normal Java probe and
-admission checks. REA does not invoke Homebrew or install a JDK. Failed
+`opt/openjdk` candidates, preferring the host architecture's prefix. Failed
 discovery probes remain available in installation diagnostics. Doctor distinguishes an absent Java
 command from a command that runs and fails, and retains bounded probe output
 and any parsed properties when the selected runtime cannot be admitted.
@@ -1199,7 +1179,7 @@ REA skill after approval. Managed registrations use the absolute selected Node o
 Bun runtime and REA entry script, including when setup ran through a package runner. Hopper
 installation remains unavailable on Windows. Setup never installs Ghidra,
 Java, or Python. It preserves valid detected Ghidra/JDK settings in agent
-registrations. See [Windows Ghidra P0](../providers/windows-ghidra-p0.md) for provider diagnostics.
+registrations. See [Windows Ghidra P0](windows-ghidra-p0.md) for provider diagnostics.

 The separate `rea mcp add` builtin delegates most clients to Incur's package-runner
 child launcher. Run that acquisition from a trusted directory; prefer managed
@@ -1317,7 +1297,7 @@ passes the deadline to each provider client; a startup failure is returned by th
 without exposing partial analysis. This deadline is separate from MCP transport
 initialization and the client's deadline for that individual tool call. A client
 can time out earlier even when Ghidra would complete within its startup deadline.
-See [Ghidra first-query deadlines and recovery](../reference/mcp-contracts.md#ghidra-first-query-deadlines-and-recovery)
+See [Ghidra first-query deadlines and recovery](mcp-contracts.md#ghidra-first-query-deadlines-and-recovery)
 for client options and the close/reopen recovery flow.

 The 330-second default can be changed on a running MCP server by setting
@@ -1370,7 +1350,7 @@ invocation instead. In MCP, `ghidra.decompile_timeout_seconds` can override the
 value for newly accepted operations on the existing Program; explicit `null`
 removes the deadline. A transient timeout remains uncached so the same function
 can be retried after an update. See the
-[settings design](../design/limits-and-recovery.md#runtime-settings-through-mcp).
+[settings design](design/limits-and-recovery.md#runtime-settings-through-mcp).
 Codex/Kimi registrations derived by `rea setup` add the selected launch value
 to the tool deadline as a single-decompile estimate; a runtime update does not
 change that registration. A bulk call can need that limit for
@@ -1433,74 +1413,6 @@ not needed for the make step, only for the Ghidra provider. If your toolchain
 rejects the inherited `-mmacosx-version-min=10.6` flag, retry the make with
 `ADDITIONAL_FLAGS="-w"`.

-### Automatically checkpoint an owned Ghidra Program
-
-On Linux/macOS, opt in with an absolute storage directory:
-
-```bash
-export REA_GHIDRA_CHECKPOINT_DIR=/absolute/rea-checkpoints
-rea decompile /absolute/target/app --procedure entry --provider ghidra --json
-```
-
-Use the same setting in the MCP server environment. CLI and MCP share the
-provider-owned implementation. The first successful analysis saves the complete
-Program as a packed `.gzf`. Later processes restore its names, comments, types
-and analysis into a private temporary project with `-noanalysis`. Normal close
-saves metadata changes; unchanged queries do not rewrite the checkpoint.
-The target executable is never executed by this workflow.
-
-For agents, `open_binary` advertises this startup setting. After selecting Ghidra,
-the default `binary_session` summary reports enabled or ephemeral mode in the
-provider's `capabilities[].shared_limitations`. Successful native results state
-whether initial analysis was created or a verified packed Program was restored.
-No separate save/restore tool or runtime analysis-setting update is required;
-enabling checkpoint mode requires the startup environment and an MCP restart.
-
-Storage is separated by target SHA-256 and analysis-profile identity, including
-the supported Ghidra version. Identical executable bytes at another path can
-reuse the Program. One live REA session holds the checkpoint's socket lease;
-a competing session reports that owner and must wait until it closes. Only
-REA-owned Programs are checkpointed. Caller-selected existing projects retain
-their separate read-only workflow below.
-
-The directory retains the current manifest and packed Program. Publication
-writes and syncs a new packed file before atomically replacing the manifest;
-superseded files are removed after publication. A failed save preserves the
-previous checkpoint and the live session for retry. Correct the reported storage
-problem, then call `close_binary` again. Incomplete cleanup retains its owner.
-Corrupt, malformed or changed checkpoints fail explicitly instead of falling
-back to a fresh import. Preserve that directory and repair it or explicitly
-select a new directory to start fresh.
-
-Recovery reaches **the last successfully saved checkpoint**. Cancellation,
-process failure or a killed CLI can lose later edits; unfinished first-time
-auto-analysis cannot resume midway. This does not restore a whole REA
-investigation, and does not promise host-crash durability. The working project
-remains ephemeral. Packed Program import, checksums, and saving consume disk and
-time proportional to Program size; saving runs once after first analysis and
-again only when the Program changes.
-
-This initial mode supports stock native ELF, PE and Mach-O imports on POSIX.
-Windows, special pinned-loader profiles, caller-selected `.gpr` projects,
-language/analyzer overrides, analysis seeds and extra analysis extensions are
-not admitted with this setting; unset it to use their existing workflows.
-The checkpoint directory must be private to the current user.
-
-REA analysis snapshots remain separate immutable query results. Initial analysis
-has a stable generation bound to the target and analysis profile: publishing its
-first checkpoint neither replaces a live MCP session nor invalidates its initial
-snapshot. Later saved states bind their content digest, so an edited checkpoint
-can require reopening without an older `--snapshot`. Snapshot import and save
-after live metadata mutation remain unavailable as before. Complete Evidence
-retains the checkpoint directory and generation in its analysis profile; restored
-reads also report the packed file's path and verified digest. Returned caveats
-distinguish restored database state from fresh analysis.
-
-Run `npm run verify:ghidra:checkpoints` with your existing Ghidra/JDK installation
-to verify fresh CLI/MCP processes, name/comment/type preservation, competing
-sessions, corruption refusal and explicit recovery. Lifecycle fixtures cover
-save failure/retry and cancellation during checkpoint finalization separately.
-
 ### Reuse an existing Ghidra project

 For repeated investigations, select an expanded local project marker with
@@ -1510,20 +1422,6 @@ in the project root; when omitted it defaults to the selected target's filename.
 Paths, globs and command flags are not program names. The matching `.rep`
 directory must be present; restore `.grez` archives with Ghidra first.

-For a `.gzf` packed program, first import it into a new Ghidra project in an
-existing, caller-selected directory. A packed program is not a `.grez` project
-archive:
-
-```bash
-"$GHIDRA_INSTALL_DIR/support/analyzeHeadless" "/absolute/new-project-directory" "new-project" \
-  -import "/absolute/program.gzf" -noanalysis
-```
-
-Select the resulting `new-project.gpr` with `REA_GHIDRA_PROJECT_PATH`. If the
-imported program name differs from the selected target's filename, set
-`REA_GHIDRA_PROGRAM_NAME` to the name reported by Ghidra's import. REA then
-opens its own read-only project copy; it does not import the packed program.
-
 ```bash
 export REA_ANALYSIS_PROVIDER=ghidra
 export REA_GHIDRA_PROJECT_PATH=/absolute/projects/app-analysis.gpr
@@ -1545,31 +1443,18 @@ the original database; REA reads selected files only for fingerprinting and copy
 This mode does not copy unrelated sibling projects, rerun repair scripts, or
 admit bridge database edits. Cleanup removes the owned copy.
 The bridge checks the program's recorded import SHA-256 against the admitted
-target digest. An unavailable or malformed recorded digest is reported as an
-unverified identity, distinct from a known mismatch; neither admits the program
-or triggers a fresh import. Select a matching target or explicitly configure a
-different project or program. Changes to the source project also fail admission;
-reopen the target to resolve a new profile after intentionally changing it.
+target digest; mismatches and project changes fail explicitly. Reopen the target
+to resolve a new profile after intentionally changing the source project.

 The profile records the caller path, resolved project/name, program and content
 fingerprint. Original analysis settings and completeness remain **unknown**;
 prior annotations or edits are caller-project state, not fresh REA discoveries.
-For supported header-selected MIPS ELF targets, the profile also binds the
-selected target's ELF metadata; it does not claim a fresh-import MIPS lane was
-used for the saved project.
 A matching recorded import digest does not claim that the database is unedited.
 Saved REA seed/analyzer reports remain historical facts in retained source Evidence;
 they are not interpreted as overrides applied by this session.
 Project content participates in snapshot identity, so different project states
 cannot reuse the same profile's cached observations.

-If a function selector is missing, use `list_procedures` or `search_procedures`
-to inspect the selected project's observed inventory. A missing entry does not
-prove the function is absent from the executable. To explicitly compare with a
-fresh import, start another REA process without `REA_GHIDRA_PROJECT_PATH` and
-`REA_GHIDRA_PROGRAM_NAME`; the fresh analysis will not include the selected
-project's annotations.
-
 To prepare a new project explicitly, use your existing Ghidra installation in a
 new directory you own (this writes that project; REA does not save it for you):

@@ -1735,7 +1620,7 @@ contains the launch arguments and `/proc/<jvm-pid>/status` reports
 session and retain the resource flags needed for the measurement rather than
 copying full command lines or environments into reports. Heap and affinity
 settings affect cost and latency; they are not part of REA's semantic analysis
-profile identity. See [real-provider testing](../development/testing.md) for bounded
+profile identity. See [real-provider testing](testing.md) for bounded
 verification workflows.

 ### Ghidra diagnostics and verification
@@ -1845,7 +1730,7 @@ Code, `codex plugin list` in Codex).
 For analysis engines, ask the connected server: have the agent call
 `binary_session` and read `result.tool_availability`, which reports what the
 server the plugin started can use, with reasons and remediation. See
-[MCP contracts](../reference/mcp-contracts.md).
+[MCP contracts](mcp-contracts.md).

 A plugin does not put `rea` on your `PATH`. To check an engine from a
 terminal, use the package runner at the version the plugin pins:
@@ -171,13 +171,6 @@ resource truncation. JavaScript summary `limitation_count` counts the full,
 deduplicated union of parent, application and semantic caveats, including messages
 whose delivery is omitted by the view's byte budget.

-Symbolic property reads and member enumeration share the expression resolver's
-existing resource budget, including recursive return spreads with fresh arguments.
-A bounded source retains independent window, preload and endpoint facts while
-reporting `parse_status: partial` and limited examination in `analysis_coverage`.
-Unresolved recursive values remain unknown; selected views retain source coverage
-separately from the completeness of the returned page.
-
 Unavailable values are represented explicitly rather than as missing fields,
 so absence of evidence cannot silently become evidence of absence.

@@ -180,7 +180,7 @@ large application can exceed one MCP response. Over MCP, pass
 the session and return only selected rows with the trace's identity and
 coverage. Page the retained trace with `inspect_analysis_view`; an oversized
 complete reply offers its first `paths` page as a ready-to-call continuation.
-See [MCP contracts](../../reference/mcp-contracts.md) for filters. A handoff binds
+See [MCP contracts](mcp-contracts.md) for filters. A handoff binds
 the exact native artifact digest and requested exports from the application
 graph. Trace direction selects the reachable addons; requested
 exports for each selected addon come from the complete supplied graph, so an
@@ -632,7 +632,7 @@ All six CLI commands accept inline JSON or a path to a JSON file. The CLI
 returns an Evidence record directly. Later workflow inputs can contain full
 records, or exact retained references when `--evidence-bundle PATH` selects an
 authenticated exported bundle. A separate CLI process has no retained MCP
-connection state. See [CLI Evidence reuse](../../getting-started/cli.md#import-export-and-compare-evidence).
+connection state. See [CLI Evidence reuse](cli.md#import-export-and-compare-evidence).

 File inputs must be regular files; symlinks to regular files are accepted.
 Directories, named pipes and device files produce an input error before JSON
@@ -665,7 +665,7 @@ References are scoped to one connection; `close_binary` clears them. Export a
 bundle before closing and import it on another connection, or supply the full
 inline Evidence there. Versions before 4.1.0 accept full inline Evidence only; installing
 newer skill instructions does not change that schema. See
-[MCP Evidence inputs](../../reference/mcp-contracts.md#retained-application-evidence-inputs).
+[MCP Evidence inputs](mcp-contracts.md#retained-application-evidence-inputs).

 For two operator-provided directories or ASARs, run:

@@ -160,7 +160,7 @@ must also satisfy the new admission. For CLI or future MCP processes, set
 `REA_ASAR_MAX_HEADER_BYTES` in the launch environment. Changing that environment
 requires a new REA process. Invalid launch values are configuration errors,
 never a silent fallback. See the
-[settings design](../../design/limits-and-recovery.md#failure-and-retry) for recovery
+[settings design](design/limits-and-recovery.md#failure-and-retry) for recovery
 metadata, precedence, and reset behavior.

 The archive index is read before any member can be selected, so
@@ -255,7 +255,7 @@ those missing bytes. New ASAR file occurrences record `unpacked: true` for
 companion files and `unpacked: false` for packed entries, including when the
 file bytes are unavailable. An omitted flag in an older inventory remains
 unknown; it does not establish either storage mode. See
-[MCP integrity handling](../../reference/mcp-contracts.md#integrity-record-and-continue) for the
+[MCP integrity handling](mcp-contracts.md#integrity-record-and-continue) for the
 tool-result contract.

 JavaScript whose syntax cannot be parsed retains unavailable semantic coverage
@@ -280,7 +280,7 @@ does not bypass ASAR header/index admission.

 If a complete response exceeds the transport budget, use its retained Evidence
 ID for a summary, module page, or item, or export the bundle. See
-[MCP tool results](../../reference/mcp-contracts.md#tool-results) for delivery limits, export, and
+[MCP tool results](mcp-contracts.md#tool-results) for delivery limits, export, and
 matching server/client buffer settings. Follow-up results also need to fit that
 budget. [Analyzer limits](#analyzer-and-result-admission) control analysis memory,
 source deadlines, and semantic capacity separately.
@@ -306,7 +306,7 @@ and caller selection remain available without implying applicable AST work.

 MCP returns a `partial_observation` retained reference after recording succeeds;
 open it with `inspect_analysis_view` on the same connection. If the SDK stopped
-waiting before receiving the reply, follow [MCP cancellation recovery](../../reference/mcp-contracts.md#progress-and-cancellation)
+waiting before receiving the reply, follow [MCP cancellation recovery](mcp-contracts.md#progress-and-cancellation)
 to find the record. CLI failure output contains the complete partial Evidence.
 Owned analyzer cleanup is verified before private files are released; uncertain
 cleanup retains ownership for retry and is reported separately.
@@ -347,23 +347,6 @@ counterparts while resolving to inventoried source files. This substitution
 requires import or require semantics. Literal Electron preload, renderer, and
 utility-process runtime paths retain the runtime filename selected by the caller.

-Application `.js` and `.ts` sources use the nearest readable, same-container
-`package.json` type; explicit module/CommonJS suffixes keep their own meaning.
-An unavailable nearer manifest leaves the package type unknown. When a module
-package contains `.js` sources, a preliminary pass through the bounded worker
-collects BrowserWindow preload declarations. Exact same-container `.js`
-preloads use the script-loader context even when their only operation is a
-helper `require`. Renderer API names alone never select that context. Dynamic,
-unresolved, excluded-source, and cross-container declarations do not establish
-a preload identity; this static association is not proof that Electron loaded
-the file. Discovery performs another static pass, while semantic projection
-runs once and existing heap, deadline, cancellation, and cleanup controls remain.
-A source that exceeds its worker limits during discovery contributes no
-declarations, and any other discovery failure ends discovery; source analysis
-then records that failure and retains partial Evidence as usual. Either gap is
-also listed in the Evidence limitations, because source analysis may still read
-that source after a declared preload has kept its package scope.
-
 Selected bounded text is then parsed as inert data to recover:

 - `package.json` metadata and declared main or renderer entrypoints;
@@ -558,14 +541,6 @@ the same artifact. Inline option syntax keeps its observed Evidence. This
 does not execute code or establish runtime configuration; popup overrides from
 `setWindowOpenHandler` are not covered by this constant-options resolution.

-A hoisted function does not establish initialization timing by declaration order.
-For classic scripts, the shared index also accounts for matching literal global
-property accesses through `globalThis`, `window`, `self`, and `this`, including
-optional and computed literal access. An early read or an indirect activation
-keeps captured options unknown even when a later bare call exists. ES module
-function declarations are not inferred to be global properties. This remains a
-bounded source-order check, not a proof that runtime activation succeeds.
-
 Recognized literal module-table bootstraps also support bounded lexical
 substitution through module exports, import helper bodies, local wrapper calls,
 returned closures, object spreads, and callback parameters. Recovered Electron
@@ -810,7 +785,7 @@ analyzer; the caller's `NODE_OPTIONS` still controls the CLI/MCP process heap.
 For defaults across new MCP operations, use `update_analysis_settings` with
 `javascript.max_heap_mb` or `javascript.analysis_timeout_ms`. Explicit per-call
 arguments take precedence, and accepted work keeps its original settings. See
-the [settings design](../../design/limits-and-recovery.md#precedence-and-lifetime).
+the [settings design](design/limits-and-recovery.md#precedence-and-lifetime).
 V8 old-space limits do not impose a process RSS limit. When REA runs on Bun,
 the analyzer ignores the V8 heap flags; resource failures then report
 `worker_heap_limit_bytes` as null instead of a requested or V8-reported limit.
@@ -149,6 +149,6 @@ non-retryable `resource_constraint` with `resource: "file-size"` and
 valid UTF-8 is an `invalid_format` request issue. These limits apply per
 operation and do not claim aggregate host containment across concurrent callers.

-See [testing.md](../../development/testing.md#javascript-source-recovery) for the focused real
+See [testing.md](testing.md#javascript-source-recovery) for the focused real
 Wakaru CLI/MCP lane and its source-owned compiler fixtures. Other host platforms
 and Bun/Vue recovery are not claimed by this adapter.
@@ -37,7 +37,7 @@ application starts, and REA never resumes it or sends
 caller-owned debugger before requesting application runtime observations.

 For a packaged Electron app, read
-[`inspect_electron_fuses`](../../electron-fuses.md) before starting an `electron-main`
+[`inspect_electron_fuses`](electron-fuses.md) before starting an `electron-main`
 target. When `EnableNodeCliInspectArguments` is disabled or removed, Electron
 ignores `--inspect` and `--inspect-brk`. A missing main-process target after
 launch does not, by itself, show that fuse.
@@ -64,11 +64,10 @@ All four preserve target-file bytes. `open_jeb_project` selects or creates an en
 - When `decompile_jeb_item` omits `unit_path`, the engine implicitly selects the project's first code unit; REA reports `unit_path: null` and a limitation instead of guessing the effective unit.
 - `item_address` is a JEB code-item reference, such as a value returned by the engine's `list_code_items`. Preserve that representation and select its code unit explicitly. For the audited CE SQLite unit, the exported method reference was `sqlite3_libversion_number`; using its raw ELF symbol address did not produce a successful decompilation. File offsets, ELF virtual addresses and engine item references have different semantics. REA currently exposes unit listing, while code-item discovery remains an upstream JEB operation.
 - Valid engine refusals (`success: false` envelopes) return `execution_failure` with the engine's message when available. Diagnostics preserve the original envelope, including any recovery advice, and the inputs of a refused primary request. If client metadata fails after a primary reply, that reply and the caller's inputs remain in partial Evidence. REA does not infer an unsupported target from a refusal, invoke a recovery tool, or retry the request.
- Successfully parsed client information is reused within the current MCP session, including when the engine omits its version. Explicit client inspection and availability probes refresh it; reconnecting invalidates the cached information.
- An unreachable endpoint is a provider-availability failure with recovery guidance; REA does not spawn the engine or automatically replay failed operations.
- After a transport or RPC failure (including a request or catalog timeout), the next explicit call attempts a new MCP connection after cleanup succeeds. Engine version and GUI mode are refreshed for that connection. Caller cancellation and decoded engine refusal envelopes preserve the existing connection.
+- Successfully parsed client information is reused for the lifetime of the MCP connection, including when the engine omits its version. Explicit client inspection and availability probes refresh it.
+- An unreachable endpoint is a provider-availability failure with recovery guidance; REA does not retry or spawn the engine.

-Real-engine verification lives in the JEB lane described in [testing.md](../development/testing.md); mock transport tests do not establish real-engine compatibility.
+Real-engine verification lives in the JEB lane described in [testing.md](testing.md); mock transport tests do not establish real-engine compatibility.

 A project-open refusal retains the selected engine-host artifact path separately
 from the service endpoint. Discovery of an unreachable service includes the same
@@ -83,7 +83,7 @@ The first text or assembly request in a session looks for this target's export i
  - Meanwhile, pseudocode comes from one `kuna decompile --addr` run. Name and address lookups, and listings, use the inventory the export takes with `kuna functions --json` before it decompiles. The session runs `kuna functions` itself, under `REA_KUNA_TIMEOUT_MS`, only when no export is building (an inventory-only request does not start one) or the export ends without an inventory.
  - Requests for the same function share one run; it stops when its last waiting request is cancelled. Each run analyzes the whole image again in its own process, so one REA process runs at most as many at once as the host has cores beyond `REA_KUNA_JOBS` (at least one). Further requests wait in order, and a waiting request is answered from the export if it finishes first. A run whose stop REA cannot prove keeps its slot until `close_binary` proves it stopped.
  - The session keeps each completed single-function text, up to 16 MiB in all with the least recently used dropped first, and answers repeats from it until the export can. After a failed export that lasts for the session.
-  - Assembly and data names wait for the export; progress notifications report the wait every ten seconds. A session does not rebuild a failed export: requests that need it fail with `retryable: false`, the export's failure, its captured Kuna output and what to change before reopening the target. REA does not expose per-function records from a failed project export, even if the retained Kuna diagnostic refers to them. Single-function fallback Evidence reports the failed state and this limitation. If cleanup remains incomplete, its error takes precedence and `close_binary` retries the retained resources. A setting such as `REA_KUNA_PROJECT_TIMEOUT_MS` or `REA_KUNA_JOBS` is read when REA starts, so changing it also needs a restart. Pseudocode keeps using single-function runs.
+  - Assembly and data names wait for the export; progress notifications report the wait every ten seconds. A session does not rebuild a failed export: requests that need it fail with `retryable: false`, the export's failure, its captured Kuna output and what to change before reopening the target. A setting such as `REA_KUNA_PROJECT_TIMEOUT_MS` or `REA_KUNA_JOBS` is read when REA starts, so changing it also needs a restart. Pseudocode keeps using single-function runs.
  - A single-function answer says so in its limitations. It lacks the export's whole-program prototypes, so a later request can return different text for the same function.

 Pseudocode, assembly, `analyze_function` and data-name answers record where their text came from in `raw_result.source`: `single-function`, or `project-export` with the cache directory. `procedure_pseudo_code` and `procedure_assembly` answers from the export also name the file, byte span and the file's SHA-256. Combined `analyze_function` answers retain both facet records in `raw_result.source.files`, each with its file, digest and byte span. Both texts come from one export; losing that project retries the complete report. Listings and procedure lookups carry no `raw_result`; omitted [Mach-O data entries](#mach-o-data-entries) are reported in their limitations. Agents can open or search the export's `.c` and `.asm` there directly when that is cheaper than calling a tool per function. Text read that way is target-derived, like any decompiler output, but it bypasses the untrusted-content marker that REA's tool results carry.
@@ -94,7 +94,7 @@ The assembly label index is scanned once per export reader. Cancelling a request

 Regex procedure and string search uses ECMAScript Unicode matching in a cancellable worker with a matching deadline and a worker old-generation heap. Literal matching remains the default. Cancellation or a matching deadline leaves the session available. The deadline is `REA_REGEX_MATCHING_DEADLINE_MS`, a positive decimal integer from 1 to 2147483647 ms. Unset uses 5000 ms. A larger value is refused because Node schedules a delay past that signed 32-bit bound as 1 ms. Invalid values are configuration errors and do not fall back to the default. The setting is read from the environment that starts REA, so a change needs a restart. A deadline failure names the effective milliseconds, whether they came from the default or the setting, the default, and the maximum. The worker old-generation heap does not raise it. The worker heap request is `REA_REGEX_WORKER_HEAP_REQUEST_MIB`, a decimal integer from 7 to 16384 MiB. Unset uses 128 MiB. A request below 7 MiB aborts the worker during startup, and a larger value is refused. Invalid values are configuration errors and do not fall back to 128. The setting is read from the environment that starts REA, so a change needs a restart. A heap failure names the effective request, whether it came from the default or the setting, the default, the floor, and the maximum. A positive Node.js `--max-old-space-size` on the process that starts REA, including `NODE_OPTIONS`, overrides that request and sets the effective heap. `--max-old-space-size-percentage` takes precedence over that flag in either order. REA does not turn the percentage into a MiB, so the effective heap stays unestablished instead of the worker heap request or the absolute flag. The reported `NODE_OPTIONS` value is the process initial environment when that block can be read. A later edit to the environment is not the value Node applied, and an unreadable initial value leaves the effective heap unestablished. The launch Node options are the initial command line on Linux when that buffer still has a program entry, not a later edit to `process.execArgv`. A preload can clear that array after V8 has applied the flags. Setting `process.title` or `--title` overwrites the command line, so a buffer without a program entry leaves the effective heap unestablished. `--env-file` or `--env-file-if-exists` can supply `NODE_OPTIONS` when the initial environment has none. That file is not part of the initial environment block, so the effective heap stays unestablished instead of the worker heap request. An initial `NODE_OPTIONS` is still used, because Node does not let the file replace it. A positive `--max-heap-size`, including the underscore form and launch `NODE_OPTIONS` on Node versions that allow it, sets the total heap rather than the old generation and can be lower than the worker heap request. The effective old generation stays unestablished while that value is in effect. A zero or empty value clears it. `--experimental-config-file` or `--experimental-default-config-file` can set `nodeOptions`, including a heap percentage, from a file that is not read back. The effective heap stays unestablished when either flag is present, including when an absolute `--max-old-space-size` is also on the command line or in the recovered `NODE_OPTIONS`. Node accepts the config path as `=` or the next argument.

-Single-function subprocess output and each cached source facet share a 16 MiB buffered-text capacity. Cached spans are checked before allocation; larger project-export spans remain in the local export and the error identifies the file and range. A single-function run does not by itself retain a complete project export. `analyze_function` with `detail: "complete"` (the CLI default) returns the complete dossier inline, which can still be large; later retained views do not remove that first transfer. The MCP default retains the dossier and returns its summary, so page the facets you need through `inspect_analysis_view`, or prefer the individual text tools for a focused question.
+Single-function subprocess output and each cached source facet share a 16 MiB buffered-text capacity. Cached spans are checked before allocation; larger text remains in the local export and the error identifies the file and range. `analyze_function` with `detail: "complete"` (the CLI default) returns the complete dossier inline, which can still be large; later retained views do not remove that first transfer. The MCP default retains the dossier and returns its summary, so page the facets you need through `inspect_analysis_view`, or prefer the individual text tools for a focused question.

 ## Mach-O data entries

@@ -147,7 +147,6 @@ that rollback is resolved; a clean rollback permits another setup attempt.

 ## Provenance and limitations

- If a completed project export reports a failed function, `procedure_pseudo_code` with `analysis: "independent_fresh"` or `rea decompile --analysis independent_fresh` requests a new single-function attempt. It bypasses the project result and prior single-function and snapshot results; it does not replace the original observation. On a cold session it obtains an inventory without starting a project export. The independent attempt can use different analysis context and may also fail. Identical results can share an Evidence ID because Evidence is content-addressed.
 - Addresses and bytes are Kuna's observations of the image. Procedure entries and extents are its derivations: extents are upper bounds clipped at the next entry, and Kuna can split one function at an entry its own analysis infers. Pseudocode is its reconstruction, never original source.
 - Pseudocode and assembly are exact Kuna text; text from Kuna and from another provider is not comparable as equal or different.
 - Results are re-read rather than replayed from REA's analysis snapshots, because a cold answer can differ from the export's.
@@ -173,7 +172,7 @@ the manifest's file identity as well as the export files. These refusal and
 migration cases are verified with controlled Kuna-format exports; they do not
 establish behavior of an independently installed Kuna release.

-Builds publish by one rename, so a reader sees a complete export or none. If later staging retirement fails, the typed cleanup error retains the completed export's key, directory and manifest in `published_export`. The session adopts that verified project; later queries reuse its immutable files while `project_export.cleanup_incomplete` reports the retained owner's live state. `close_binary` retries only the remaining cleanup, and a successful retry resolves prior cleanup errors. A failed export followed by failed staging cleanup retains both failures; it does not invent a publication receipt. A session keeps the export it uses from eviction only within its own REA process. If another REA process sharing the cache evicts it, the session rebuilds it; meanwhile pseudocode falls back to single-function runs. A damaged or edited export is removed and rebuilt. REA retains the file state verified with each digest, checks it before warm-cache reuse, and checks open descriptors before and after reading text. Assembly indexes are checked against the same state; a changed file makes the whole report retry rather than mixing facets from different exports. Staging moves to `trash/` for removal only after REA proves its Kuna process stopped. Staging of a process it cannot prove stopped is never swept; REA keeps it owned, retries the stop on `close_binary`, and reports it until the stop is proven; that MCP error names the same-connection retry as `recovery.kind=retry_cleanup` ([retained cleanup retry](reference/mcp-contracts.md#retained-cleanup-retry)). Failed file removal also stays bound to its export and is retried by `close_binary`; closing does not report success while that cleanup remains. `rea doctor --provider kuna` reports the cache directory without creating it.
+Builds publish by one rename, so a reader sees a complete export or none. If later staging retirement fails, the typed cleanup error retains the completed export's key, directory and manifest in `published_export`. The session adopts that verified project; later queries reuse its immutable files while `project_export.cleanup_incomplete` reports the retained owner's live state. `close_binary` retries only the remaining cleanup, and a successful retry resolves prior cleanup errors. A failed export followed by failed staging cleanup retains both failures; it does not invent a publication receipt. A session keeps the export it uses from eviction only within its own REA process. If another REA process sharing the cache evicts it, the session rebuilds it; meanwhile pseudocode falls back to single-function runs. A damaged or edited export is removed and rebuilt. REA retains the file state verified with each digest, checks it before warm-cache reuse, and checks open descriptors before and after reading text. Assembly indexes are checked against the same state; a changed file makes the whole report retry rather than mixing facets from different exports. Staging moves to `trash/` for removal only after REA proves its Kuna process stopped. Staging of a process it cannot prove stopped is never swept; REA keeps it owned, retries the stop on `close_binary`, and reports it until the stop is proven; that MCP error names the same-connection retry as `recovery.kind=retry_cleanup` ([retained cleanup retry](mcp-contracts.md#retained-cleanup-retry)). Failed file removal also stays bound to its export and is retried by `close_binary`; closing does not report success while that cleanup remains. `rea doctor --provider kuna` reports the cache directory without creating it.

 ## Verify with a real Kuna

@@ -184,7 +183,7 @@ REA_KUNA_COMMAND=/absolute/path/to/kuna GHIDRA_INSTALL_DIR=/absolute/path/to/ghi
  npm run verify:kuna -- --targets DIR --functions inflate,crc32 --compare-ghidra
 ```

-The lane compiles a small source-owned fixture with the host C compiler and verifies the MCP workflow end to end. `--targets DIR --functions a,b` adds caller-built binaries. `--compare-ghidra` (with `GHIDRA_INSTALL_DIR`) runs those same functions through Ghidra; it requires `--targets` and `--functions` and refuses empty matrices or requested function names missing from every target. The report lists examined caller binaries and their matching requested symbols, including inputs omitted from analysis. See [testing](development/testing.md#kuna-lane) for coverage.
+The lane compiles a small source-owned fixture with the host C compiler and verifies the MCP workflow end to end. `--targets DIR --functions a,b` adds caller-built binaries. `--compare-ghidra` (with `GHIDRA_INSTALL_DIR`) runs those same functions through Ghidra; it requires `--targets` and `--functions` and refuses empty matrices or requested function names missing from every target. See [testing](testing.md#kuna-lane) for coverage.

 Failed runs also report process-lineage evidence and exit unsuccessfully. If provider or transport cleanup is unconfirmed, the report says `cleanup: "incomplete"` and records `retained_workspace`; that directory is preserved for investigation and cleanup retries.

@@ -24,7 +24,7 @@ Native-body bridge mapping and managed runtime execution are outside the
 current tool set.

 The canonical tool inventory is the
-[build-generated catalog](../../reference/mcp-contracts.md#generated-catalog).
+[build-generated catalog](mcp-contracts.md#generated-catalog).

 ## Inspect an assembly

@@ -245,13 +245,13 @@ The canonical parser admits PE/CLI bytes and their metadata/CIL without loading
 an assembly. It reports observed implementation markers and unavailable facts;
 it does not itself unpack .NET single-file hosts or infer a NativeAOT identity
 from an ordinary native PE. It does not decode IL2CPP; use
-[IL2CPP metadata](../../il2cpp-metadata.md) for the image, type and method names in a
+[IL2CPP metadata](il2cpp-metadata.md) for the image, type and method names in a
 Unity `global-metadata.dat`. Inputs without admitted CLI metadata do not
 become managed assemblies through naming or routing guesses.
 Inspect separately obtained components explicitly and preserve their identities.

 For ordinary .NET single-file hosts, use the existing artifact tools to
-[inventory and extract bundle members](../../dotnet-bundles.md), then inspect the
+[inventory and extract bundle members](dotnet-bundles.md), then inspect the
 extracted assembly explicitly with the managed tools.

 A valid implementation marker establishes a candidate native boundary, not
@@ -280,21 +280,6 @@ inspects its two selected paths sequentially, retaining each inspection rather
 than both full byte snapshots. The limit therefore remains a per-file resource
 admission rule, not an aggregate comparison limit. Comparison Evidence keeps
 the caller-selected paths as its parameters and artifact locations.
-When either side's member inspection exceeds its representation budget, the
-comparison limitations name that side and its `resource-limit` diagnostic; its
-empty member collections do not establish added or removed members. Each side's
-`resource_limits` preserves the reported diagnostic's code, scope, detail and
-nullable offset. An empty array means no resource limit was reported; historical
-comparisons omit this field, leaving those diagnostics unrecorded. Always read
-the comparison coverage alongside member counts. To compare
-a smaller selection, pass the same repeatable `--type` full names that
-`inspect-managed-members --type` accepts to `compare-managed-members`, which
-applies them to both sides and records them as `type_names`; over MCP, compare
-two `inspect_managed_members` Evidence records selected with the same
-`type_names`. A single selected type can still exceed the budget.
-The two-record MCP workflow keeps full source Evidence available for
-`inspect_analysis_view` field selection and paging; path-based CLI comparison
-records the selected paths, type names and per-side diagnostics.

 Input overflow returns a resource constraint. Decode or projection overflow
 reports `resource-limit` with unavailable or partial coverage; omitted facts do
@@ -608,13 +593,13 @@ describes exported shared-library entry points.
 REA offers a built-in read-only snapshot parser for x64 PE/RTR 9.1 metadata and
 an optional Linux headless Ghidra adapter for annotations and broader recovery.
 The adapter requires a locally built `REA_GHIDRA_NATIVEAOT_JAR`; REA does not
-install it or its toolchain. The [NativeAOT guide](../../providers/ghidra-nativeaot.md) defines
+install it or its toolchain. The [NativeAOT guide](ghidra-nativeaot.md) defines
 these routes, their layout/host restrictions, derived-memory provenance, and
 verification coverage.

 REA's experimental Windows Ghidra boundary admits native x86, x86-64, ARMNT (Thumb-2) and ARM64 PE
 applications and DLLs for static analysis. For x64 PE NativeAOT, the read-only
-parser also runs there; the [NativeAOT guide](../../providers/ghidra-nativeaot.md) lists what a
+parser also runs there; the [NativeAOT guide](ghidra-nativeaot.md) lists what a
 Windows host covers.

 For NativeAOT analysis, preserve the selected native artifact's path and digest
@@ -623,7 +608,6 @@ to native function addresses requires verified
 provider evidence; names or vtable similarity alone do not prove that a native
 function implements a specific managed method.

-<div id="managednative-boundary-rules"></div>
 <div id="managed-native-boundaries"></div>

 ## Managed/native boundary rules
@@ -678,7 +662,7 @@ partial when unknown MethodDef ownership can hide a selected body.
 Metadata tokens are not native addresses. Native body mapping for C++/CLI,
 ReadyToRun, NativeAOT, and IL2CPP requires separately verified format and provider
 support. The managed static tools do not recover those mappings. The optional
-[Ghidra NativeAOT extension](../../providers/ghidra-nativeaot.md) has its own supported boundary.
+[Ghidra NativeAOT extension](ghidra-nativeaot.md) has its own supported boundary.

 Declared import inventory supports a bounded positive claim. Its absence does
 not exclude dynamic resolution, generated code, protected code, native helpers,
@@ -740,10 +724,6 @@ refer to the pointer table when present rather than necessarily contiguous
 definition rows. Invalid or nonmonotonic list coordinates and malformed or
 ambiguous pointers leave affected owners unknown with partial coverage while
 preserving readable member and attribute facts.
-For each list column, ordering checks compare consecutive valid coordinates
-even across invalid rows. A provable decrease leaves the affected ownership
-unknown. Retained declaring-type filters count these candidates in
-`unresolved_filter_rows`; omit that filter to retrieve their known-name rows.
 The retained inverse indexes are admitted against the existing representation
 budget before allocation.

@@ -850,7 +830,7 @@ Target platform is not host support. The canonical parser must inspect
 Windows-produced PE/CLI bytes on REA's supported Linux and macOS hosts with the
 same result. Pinned Windows oracle jobs may provide additional conformance, but
 do not establish that the REA managed analysis workflow has been verified on a
-Windows host. The [experimental Windows Ghidra boundary](../../providers/windows-ghidra-p0.md)
+Windows host. The [experimental Windows Ghidra boundary](windows-ghidra-p0.md)
 has its own host and provider verification scope. Native
 ReadyToRun, C++/CLI, NativeAOT, or IL2CPP coverage is additionally constrained
 by the selected Hopper/Ghidra host and format matrix.
@@ -861,7 +841,7 @@ The current lane uses source-owned byte-built fixtures and malformed-input
 regressions, with optional operator-supplied applications and ILSpy verification.

 Run the deterministic lane with `npm run verify:managed`. See
-[testing](../../development/testing.md#real-toolchain-verification-lanes) for prerequisites and
+[testing](testing.md#real-toolchain-verification-lanes) for prerequisites and
 coverage. Generated outputs belong outside tracked fixture directories and must
 not remain after verification or packaging.

@@ -1,140 +0,0 @@
-# Measure MCP catalog costs in Codex
-
-Use actual harness usage to evaluate catalog changes. A `tools/list` JSON byte
-count measures transport size. It does not establish how many tokens a client
-submits to a model, whether it defers schemas, or the total cost of an analysis.
-The pinned [Codex observations](verification/mcp-catalog-codex-2026-11-05.md)
-include actual loading controls, an unavailable-host negative control and a
-completed real-package pilot.
-
-## Run a controlled loading comparison
-
-Build the selected source checkout with the pinned Node and npm versions first:
-
-```sh
-npm ci
-npm run build:cached
-npm run eval:mcp-catalog -- --model gpt-6.1-sol \
-  --output "$HOME/.cache/rea-catalog-run" --repetitions 3 --plan
-```
-
-Remove `--plan` to execute the matrix. This makes real model requests using the
-local Codex authentication. The output directory must not already exist. No
-account configuration is changed. The runner copies only authentication into
-an external disposable profile and removes that profile after each trial.
-Execution stays outside both source checkouts even when results are saved inside
-one, so ancestor repository instructions and skills do not pollute the trial.
-The npm entrypoint holds the driver's artifact lock throughout the matrix. A
-selected external checkout has its own lock, so the matrix also pins one runtime
-fingerprint and binds its catalog receipt to that manifest. Freshness checks
-stop further model calls if the runtime changes between trials. Each trial's
-before/after fingerprints must match the matrix pin; different builds never form
-a valid pair. Matrix admission/freshness audits sit outside individual guarded
-trial resource measurements. Do not rebuild the selected runtime concurrently.
-
-This lane requires Linux, Python 3, a working user systemd manager with cgroup v2,
-and an installed Codex CLI supporting the recorded flags. It reuses the existing
-resource observer: one CPU, 4 GiB hard memory limit, 3 GiB early stop, no swap,
-and a 192-task ceiling. Runs are sequential. Unsupported clients, resource stops,
-failed startup, missing usage, and unverified cleanup remain failed measurements.
-They do not become zero-cost successes.
-
-Trials disable account apps and plugins explicitly. A fresh `CODEX_HOME` alone
-does not prevent account-connected tools from appearing in the client executor
-catalog. For a deliberate mixed-catalog investigation, run `agent-trial.py` with
-`--include-account-tools`; keep those results separate from REA-only trials.
-The settings receipt records the same feature policy written to Codex config.
-
-Each repetition compares no server, all REA tools, and a client-selected subset
-(`binary_session` by default), in the supported client-code host mode. Alternate
-repetitions reverse ordering. All variants receive the same developer instructions
-and exact-response prompt. A valid loading trial completes one turn, returns
-`CATALOG_OK`, and performs no tool calls. REA is marked `required` in every
-server-enabled configuration. The runner explicitly disables/enables the stable
-`code_mode_host` feature for direct/client-code modes. The old `code_mode` and
-`code_mode_only` switches do not override Codex 0.165's enabled host default.
-The requested flags and CLI version are retained; verify the actual call shape
-in completed-task traces too. `--modes direct client-code` adds a diagnostic
-host-disabled control. This installed Codex reports that disabling the host
-makes tool dispatch unavailable; it does not provide a qualified eager/direct
-comparison. An empty response alone cannot qualify tool availability. Errors
-invalidate that profile even when the model still emits the expected marker.
-
-Useful controls:
-
-```sh
-# Compare full input guidance with the default compact input presentation.
-npm run eval:mcp-catalog -- --model gpt-6.1-sol \
-  --output "$HOME/.cache/rea-catalog-full" --input-profile full --repetitions 3
-
-# Choose exact tool names in the working host mode.
-npm run eval:mcp-catalog -- --model gpt-6.1-sol \
-  --output "$HOME/.cache/rea-catalog-selected" --modes client-code \
-  --selected-tools analyze_javascript_application inspect_analysis_view
-```
-
-`enabled_tools` filters the catalog after client discovery. It does not reduce
-the server's original `tools/list` transport. Server tool-family scope is a
-separate existing control; do not attribute client filtering results to it.
-The output-schema profile remains REA's default in these experiments.
-
-## Read the evidence
-
-`report.json` retains every attempted trial and compares each enabled-server
-trial with its same-mode, same-repetition no-server control. It reports valid
-pair counts and the median/range of observed input-token differences. Failed
-pairs are explicit and excluded from the median. A small or negative delta can
-reflect client framing, randomized workspace paths, and measurement variation;
-it does not establish a negative schema cost.
-
-Usage, cleanup and resource receipts are collected independently of the verdict.
-A failed host, malformed event or wrong marker can retain observed usage and
-resource costs. Stage-specific issues explain invalidity; missing observations
-remain unknown. A changed matrix records its unattempted cells explicitly.
-
-Each trial retains its exact prompt, runtime file digests, requested model alias,
-Codex version, settings/source hashes, JSONL events, actual usage, answer, cleanup
-receipt, and process-family resource receipt. The selected rollout capture keeps
-per-response usage and tool exchanges; authentication, ambient environment,
-account metadata, and encrypted reasoning are excluded. Tool output and local
-paths remain evidence and should be reviewed before sharing the raw files.
-
-The metrics have distinct meanings:
-
-| Metric                              | Meaning and limit                                                                                               |
-| ----------------------------------- | --------------------------------------------------------------------------------------------------------------- |
-| Catalog bytes and SHA-256           | Built server advertisement, including output schemas; not model input.                                          |
-| `turn.completed.usage.input_tokens` | Observed whole-turn usage reported by Codex; includes cached input.                                             |
-| Cached/uncached input               | Report both. Cache hits do not remove tokens from the context.                                                  |
-| Per-response usage                  | Retained usage records help locate discovery and continuation costs. Do not add cumulative thread counts again. |
-| Paired input delta                  | Incremental loading observation including instructions/client framing; not an exact schema-only token count.    |
-| Elapsed and family CPU              | Whole guarded trial, including local setup and client/network waits; remote inference CPU is unmeasured.        |
-| Family peak memory                  | Kernel cgroup peak at payload exit, including observer and file cache; not final whole-scope counters.          |
-
-These are fresh client/server sessions. OS caches and API prefix caches can
-already be warm. No cold-cache claim follows from a new session. The requested
-model alias is recorded; a resolved server-side model version is not inferred.
-The harness usage is not an independent billing reconciliation.
-The usage event shape follows the documented
-[Codex non-interactive JSON output](https://developers.openai.com/codex/noninteractive#make-output-machine-readable).
-
-## Evaluate completed investigations too
-
-A no-tool response can avoid deferred discovery entirely. Before changing the
-catalog based on this lane, compare completed tasks through the real harness.
-Use `npm run verify:agent` and its known-answer rubric, or run a selected real
-artifact through `tests/support/analysis-efficiency/agent-trial.py` under
-`resource-run.py --observe-payload-exit`. Use the same task, artifact digest,
-model/reasoning, authority, result coverage, and correctness oracle in every arm.
-The existing runner accepts exact `--enabled-tools` and defaults to client-code
-host mode. Its direct option is a host-disabled diagnostic, not a claim of
-working native dispatch in the installed client.
-Use `--capture-tool-context` to locate per-response costs. Its task summary
-explicitly leaves factual correctness unassessed until an independent oracle or
-transcript review establishes the requested facts.
-
-Count discovery, arguments, replies, retries, and continuations. Check the
-requested facts against source bytes or another independent oracle, real produced
-Evidence IDs and source links, partial/unknown coverage, and cleanup. Preserve
-failed attempts. A successful small-package task is a pilot, not proof of broad
-application performance or provider compatibility.
@@ -1,7 +1,7 @@
 # MCP runtime contracts

 For pairing native functions before comparing selected dossiers, see
-[native function matching](../native-function-matching.md). It operates on retained
+[native function matching](native-function-matching.md). It operates on retained
 inventories, preserves aliases/unknowns and exposes selected fact pages.

 Use this reference to call REA tools and interpret their replies on one MCP
@@ -129,15 +129,7 @@ side declares a required facet unavailable. An empty legacy facet without a
 coverage declaration is also unknown. A producer that actually observed an
 empty facet can declare it available so observed absence remains comparable.
 Call comparison additionally retains the Evidence relationship coverage
-checks. Its call status compares the provider-observed sets; discovery
-limitations stay on that dimension even when the observed sets match or differ.
-The calls dimension's `discovery_status` records whether discovery is complete,
-partial, or unknown across both sides and directions; older comparisons may omit
-it. Incomplete or unreported discovery also remains a residual unknown and an
-unresolved `find_changed_behavior` finding, including when observed sets match.
-A structural reconstruction claim about calls remains unknown unless both
-directions have established static direct-call discovery. An independent
-observed change in another dimension can still fail an overall claim. Ghidra and Hopper declare their observed dossier facets and complete
+checks. Ghidra and Hopper declare their observed dossier facets and complete
 provider-observed caller/callee sets, including empty sets. Missing decompiler
 output remains unavailable; complete call coverage does not claim every runtime
 target. When Ghidra's decompiler fails on one function, its dossier is still
@@ -196,11 +188,7 @@ The complete field/type diagnostic is preserved when normalization fits the
 response budget, including request-specific rejected fields and reasons. Zod
 input issues retain their field paths and available type and range constraints.
 SDK diagnostic parts may be distributed between field issues and the main
-message so each retained explanation appears once. Known neighboring-tool
-argument-name mistakes (such as `address` instead of `procedure`, or `query`
-instead of `pattern`) provide targeted replacement guidance and the expected
-canonical property name without accepting unauthorized aliases or changing
-canonical Evidence parameters.
+message so each retained explanation appears once.
 If their conservative projection allowance is exhausted, the response states
 that field-level detail was omitted and retains the original SDK diagnostic.
 Oversized SDK diagnostics keep the existing retained-Evidence recovery path. An unknown
@@ -214,18 +202,11 @@ relationship coverage and read-specific `limitations`, alongside observed
 `calls`. When a provider does not classify its caveats, they remain on that
 node and coverage is `unknown`. An empty call list with partial or unknown
 coverage is not proof that the function has no calls.
-`trace_call_path` reports limited relationship reads in `residual_unknowns` and
-sets `truncated: true`; any path supported by observed edges remains visible.
-`search_scope.observed_goal_status` describes the search of the provider-observed
-graph, while `search_scope.discovery` describes whether discovery of applicable
-direct relationships is established. A missing goal is `unknown` when either
-discovery or a relationship read is unestablished. A found path is shortest
-within the observed graph; undiscovered calls may produce a shorter path.
-`truncated` describes relationship reads, not unestablished discovery.
-`build_call_path` applies the same distinction to supplied function Evidence:
-its `search_scope.exhaustive` describes the supplied graph and
-`search_scope.observed_status` preserves that graph's result. Evidence without
-discovery metadata has unknown discovery. Cancellation remains a tool error.
+`trace_call_path` reports each limited expansion in `residual_unknowns` and
+sets `truncated: true`; any path already supported by observed edges remains
+visible. When a requested goal is not reached but an expansion is unresolved,
+`goal_status` is `unknown`; `not_reached` means traversal exhausted without
+unresolved relationship reads. Cancellation remains a tool error.

 `trace_feature` validates each reference's containing-procedure resolution using
 the same contract as navigation context. Explicit absence remains a successful
@@ -252,11 +233,10 @@ restart or recreate the server to apply changes. If a result cannot fit, REA ret
 `resource_constraint` with `details.resource: "transport"` before constructing
 a document-sized string. Analysis Evidence remains complete in the current
 session. Its exact reference is reported in
-`details.reported_limits.evidence_reference`; for supported parent operations,
-call `inspect_analysis_view` with that reference and a compatible view. To recover
-any retained record, export the complete session with `export_evidence_bundle`
-to a destination path. Complete bundle exports stream canonical JSON into an
-atomically published file.
+`details.reported_limits.evidence_reference`; call `inspect_analysis_view` with
+that reference for a summary, one section/module, or a stable page, or call
+`export_evidence_bundle` with a destination path. Complete
+bundle exports stream canonical JSON into an atomically published file.

 On protocol revision `2026-07-28`, completed replies retain the SDK's
 `resultType: "complete"`, including the replacement for an oversized error.
@@ -304,17 +284,6 @@ to `/absolute/view-request.json`, then run
 `rea inspect-analysis-view /absolute/view-request.json --json`. This also reads
 pre-summary source records without changing their identity; no live provider is started.

-Unavailable or inapplicable native collections keep `items.rows: null` and
-report `coverage: {"status":"unavailable","examined":0,"total":null,"next_offset":null,"exhausted":false}`.
-This applies to unrecorded `native-load-image` checks/sections and inapplicable
-`native-context` result limitations. Their total is unknown; no continuation is
-offered. Stop paging that collection and inspect the returned unknowns rather
-than treating it as an observed empty set or retrying a null offset. Recorded
-empty collections, empty selections and offsets past the end retain numeric
-totals and exhausted page coverage. Clients upgrading from the earlier
-zero-total representation must handle the new `unavailable` status and nullable
-total; historical saved views remain valid.
-
 `procedure_address`, `procedure_callees`, `procedure_callers`,
 `resolve_containing_procedure` and `get_call_graph` also accept `detail: "summary"`
 (complete remains the default). The summary includes the first 64 recorded
@@ -334,8 +303,6 @@ Retained `xrefs` Evidence also supports `native-observation` address pages and
 default and does not accept `detail`; when its MCP response exceeds the budget,
 follow the returned continuation to page the retained result. These addresses
 remain untyped; paging does not add reference kinds or establish completeness.
-The page tells callers that any additional provider detail recorded in the parent
-requires retrieving or exporting the complete Evidence.

 These views reference complete source context through `source_context.digest`
 and caveat counts. Read it using the same parent with
@@ -353,17 +320,6 @@ unknown. Exhausted pages describe the recorded observations and do not establish
 complete native discovery. The same views work through the CLI with historical
 Evidence files or bundles and require no live provider.

-For retained `inspect_native_instruction` Evidence, use
-`view: {"kind":"native-instruction-references","collection":"incoming_references","offset":0,"limit":64}`
-to page typed references to the exact code or data address. Select `references`
-for outgoing instruction references. Rows preserve their original indices and
-provider-reported kind and provenance. `items.state` distinguishes available,
-unavailable, and not-recorded collections; coverage is null in the latter two
-cases. The fixed 1 MiB page projection allowance leaves room for Evidence and
-MCP encoding. An oversized single row remains in the complete parent, which
-can be exported. Page exhaustion describes retained rows, not discovery or
-runtime access.
-
 For oversized native function Evidence, `details.reported_limits.continuation`
 contains a ready-to-call `inspect_analysis_view` request for the retained
 pseudocode's first page. Use its `name` and `arguments` directly, then follow
@@ -385,18 +341,9 @@ To discover existing records without their large payloads, call
 `get_evidence_bundle` with `detail: "summary"`. Its `result.records` contain
 Evidence IDs, artifact/provider identities, analysis-profile digests and native
 procedure metadata. Optional `filters` match exact `evidence_id`, `operation`,
-`target_sha256`, `analysis_profile_digest` or `procedure_address`. For a supported
-parent operation, use a discovered ID with a compatible `inspect_analysis_view`;
-neither discovery nor retained selection starts a provider. For records without
-a supported view, use `detail: "records"` to retrieve selected complete records,
-or export the bundle to a caller-selected path. Record and bundle delivery are
-subject to the MCP response budget. Summary rows are not complete records.
-Retained `procedure_pseudo_code` Evidence supports `summary` and
-`native`/`pseudocode` views of the original observation, including
-`view: {kind: "native", facet: "pseudocode", offset: 0, limit: 4096}`;
-pages do not start a provider or create another decompilation. An
-`analyze_function` dossier is a different observation.
-`retention: "complete-record"` describes stored Evidence, while
+`target_sha256`, `analysis_profile_digest` or `procedure_address`. Use a discovered
+ID with `inspect_analysis_view`; neither discovery nor retained selection starts
+a provider. `retention: "complete-record"` describes stored Evidence, while
 `native_dossier.value_flow` independently reports truncation, unavailable or
 unknown metadata. Missing omission counts remain null. Summary output carries
 every matching record; actual transport admission still applies. Omitted
@@ -446,31 +393,10 @@ Automatically retained workflow questions include their immutable result
 Evidence ID. Distinct results retain independent questions and source links;
 repeating the same result does not create another unknown. Workflow Evidence
 keeps the original residual question text. Explicit `record_unknown` requests
-keep caller-selected identity and reject duplicate creation. Explicit creation
-uses the active binary analysis target digest as `scope_digest`, or null when
-there is no active target. Supporting Evidence does not select the scope. Scope
-contributes to the stable unknown ID, so the same question can have different
-IDs under different scopes. Check the active target before recording a
-target-scoped unknown; creating one in a target-free session does not infer a
-target from its supporting Evidence.
+keep caller-selected identity and reject duplicate creation.
 Duplicate creation is a nonretryable `invalid_request`; use the existing head
 or update it with its current `expected_revision`. A stale update remains a
-retryable `revision_conflict`. An `update_unknown` revision keeps the unknown’s
-original `scope_digest`. Its mutation Evidence subject is the active binary
-analysis target, or null without one, so it can differ from the unknown’s scope.
-
-If automatic question publication fails after a workflow completes,
-`details.workflow_unknown_publication` identifies the Evidence and states
-whether its retention was confirmed. `created_questions` and
-`existing_questions` count processed question occurrences; duplicate questions
-may share an Unknown identity. `total_questions` counts string questions, and
-`next_question_index` is the zero-based position in the workflow's original
-`residual_unknowns` array where publication stopped. It is not a resume token.
-For a retained record on the same MCP connection, retrieve the Evidence by ID
-with `get_evidence_bundle` and inspect committed heads with `list_unknowns`.
-Unprocessed questions remain in the completed Evidence; they were not checked
-by this attempt and may already exist from earlier work. A one-shot invocation identifies session-only retention
-as `invocation-only` and carries the completed Evidence in its failure when available.
+retryable `revision_conflict`.

 When `record_unknown` or `update_unknown` commits but its complete reply exceeds
 the response budget, `details.reported_limits.committed_unknown` identifies the
@@ -586,12 +512,10 @@ result's `_meta`, whether the call succeeded or failed:
 ```

 The marker is declared once per tool contract (`returnsTargetContent`) and is
-on by default: `inspect_analysis_settings`, `update_analysis_settings`,
-`export_evidence_bundle`, `record_unknown`, `guided_workflows`,
-`search_guidance`, and `read_guidance_section` omit it. The first four contain
-only REA session state or caller-supplied values; the workflow and guidance
-tools return REA's own installed workflows and documentation, not text from an
-analysis target. Tools whose results or errors
+on by default: `export_evidence_bundle`, `record_unknown`, `search_guidance`,
+and `read_guidance_section` omit it. The first two contain only REA session
+state or caller-supplied values; the guidance tools return REA's own installed
+documentation, not text from an analysis target. Tools whose results or errors
 can include provider, launcher, or device output stay marked, including
 `binary_session` (provider failure
 reasons and availability diagnostics), `close_binary` (provider cleanup
@@ -611,21 +535,6 @@ that the response budget accounts for. It does not alter `content` or
 such as requiring approval for process-launching or device-mutating tools
 after target content was read.

-## Offline API contract declarations
-
-`inspect_api_contract` reads local OpenAPI 3.0/3.1/3.2 JSON (default) or
-GraphQL SDL (`format: "graphql-sdl"`) without an active target or network requests.
-OpenAPI inventories inline path operations and unresolved Path Items. GraphQL
-inventories type/field declarations; optional `operations_path` adds operation
-owners, aliases, SDL field bindings and explicit fragment-spread edges without
-expanding fragments. Unresolved bindings and unavailable models stay explicit.
-Default summaries retain complete Evidence; `api-contract` or `graphql-contract`
-views select facts immediately with exact filters, fields and paging. Retained
-`inspect_analysis_view` uses the same projector without reopening inputs.
-Coverage describes examined declarations and does not establish runtime behavior
-or full specification/operation validity. See [offline API contracts](../api-contracts.md)
-for source identities, parser allowances, supported scope and CLI publication.
-
 ## Retained application Evidence inputs

 `analyze_javascript_application`, `inspect_binary_layout`, `inspect_artifact`,
@@ -654,7 +563,7 @@ grouping request lines by method, origin and format-rule path template. Template
 segments are inferences. Because paging follows the full grouping, every page is
 inferred Evidence whenever any group is templated, and derived Evidence only when
 no group was templated.
-See [derived API surfaces](../guides/web/web-network-captures.md#derived-api-surface).
+See [derived API surfaces](web-network-captures.md#derived-api-surface).

 `inspect_analysis_view` also accepts `environment-manifest` for retained HAR capture
 Evidence and `capture_browser_scenario` Evidence, projecting the primary origin's request lines into named tools with path
@@ -662,14 +571,14 @@ templates, parameters, observed query names, value-free body shapes and record
 pointers, plus excluded groups and three fixed unknowns. Templates, parameters and
 names are inferences; the Evidence is inferred whenever any tool or excluded group
 is templated, and derived otherwise.
-See [environment manifests](../guides/web/web-network-captures.md#environment-manifest).
+See [environment manifests](web-network-captures.md#environment-manifest).

 `inspect_analysis_view` also accepts `environment-state` for the same parents,
 extracting the initial state the recorded reads observed: entity types with an
 identity field, entities, documents for non-entity reads, and a render
 plan per read tool that reproduces its recordings from the state or names why it
 cannot. Types and identity are inferences, so the Evidence is always inferred.
-See [environment state](../guides/web/web-network-captures.md#environment-state).
+See [environment state](web-network-captures.md#environment-state).

 `inspect_analysis_view` projects a caller-selected view of already completed
 `inspect_binary_layout`, `analyze_javascript_application`, or `analyze_function`
@@ -680,14 +589,7 @@ and limit default to 0 and 64; pseudocode uses UTF-16 code units and never
 splits surrogate pairs, while other pages count rows. Unavailable facts and
 provider limitations remain explicit. Source is
 an exact same-session retained reference, portable inline Evidence, or an
-Evidence record or bundle file. When Evidence retention is available, inspecting
-a caller-supplied inline or file source retains the resulting view in the active
-MCP session; it does not automatically retain the caller-owned parent. To use
-`parent_evidence_id` in later retained queries, import a bundle containing the
-parent into that session. Alternatively, supply the inline or file source again
-for each view; doing so does not make the parent available for retained lookup.
-An embedded or fixed-target server without a session does not retain the view;
-keep the returned Evidence if it is needed later. Native function, inventory, and observation
+Evidence record or bundle file. Native function, inventory, and observation
 views require the `rea.analysis` predicate; function-matching views require
 `rea.native-function-matching`. A mismatched predicate returns an
 `invalid_request` identifying `source.predicate_type`. Views are
@@ -766,19 +668,12 @@ refuses the summary before analysis. Further views use the returned
 `parent_evidence_id` through `inspect_analysis_view`, or a saved Evidence file or
 portable bundle, and never repeat decompilation.

-A null provider observation produces `status: "unavailable"` and
-`reason: "no_pseudocode"`; item limitations retain any provider explanation.
-This does not establish why pseudocode is absent or whether a retry would help.
-Operation failures and malformed non-null output remain `status: "error"`.
-The `failed` count includes both unavailable and error items. Existing retained
-records keep their original item statuses and error details.
-
 A `batch-decompile` view selects one `collection` and repeats the batch counts
 and provider identities:

 - `items`: rows in retained order with their original `index`, so duplicate
  selectors stay distinct. A row keeps the selector in `address`, its `procedure`
-  identity and `status`, plus `pseudocode_code_units`, an unavailable `reason`, or its exact `error` and
+  identity and `status`, plus `pseudocode_code_units` or its exact `error` and
  `limitations`. `where.indices`, `where.addresses`, `where.procedure_addresses`
  and `where.statuses` filter exactly and combine; an item with unknown identity
  never matches `procedure_addresses`. Omitted filters select all, and empty
@@ -787,11 +682,11 @@ and provider identities:
 - `pseudocode`: one `index`'s text in UTF-16 code-unit pages. `offset` and `limit`
  default to 0 and 16,384, and `coverage` measures that body. An offset inside a
  surrogate pair is refused, and a limit ending inside one stops before it. An
-  unavailable or error item has no text and is refused with a pointer to `items`.
+  error item has no text and is refused with a pointer to `items`.

 Page `coverage` counts the selection only: exhausting it establishes nothing
 about functions outside the batch. Evidence `limitations` aggregate every item's
-provider observations and are not attributed to one successful item; unavailable and error
+provider observations and are not attributed to one successful item; only error
 items keep their own. A page over the response budget offers a smaller selection
 from the same `source`: fewer rows, or one body's `pseudocode` pages when a single
 row does not fit. An inline source offers none, because the record cannot be
@@ -878,7 +773,6 @@ arrays and nested sources declared by the tool's input schema:
 | `match_native_functions`                                                                                    | `left`, `right`, `left_observations[]`, `right_observations[]`                                                        |
 | `trace_application_feature`, `trace_javascript_semantics`, `compare_source_to_bundle`                       | `application`; feature tracing also accepts `native_observations[]`                                                   |
 | `compare_application_versions`, `compare_javascript_export_shapes`                                          | `left`, `right`; version comparison also accepts both native-observation arrays                                       |
-| `compare_static_and_observed_endpoints`                                                                     | `application`, `capture`; summary retains the complete comparison for `endpoint-comparison` pages                     |
 | `reconcile_javascript_runtime`                                                                              | `static_layers[].analysis`, `runtime_observations[]`                                                                  |
 | `compare_managed_members`, `verify_managed_native_boundaries`, `import_managed_reconstruction`              | Comparison `left`/`right`; verification `managed_boundaries`/`native_observations[]`; reconstruction `static_members` |
 | `project_managed_application_graph`                                                                         | `managed_artifact`, `managed_members`, `managed_native_boundaries`                                                    |
@@ -938,7 +832,7 @@ CLI workflows that advertise `--evidence-bundle` can resolve the same reference
 JSON from one explicitly selected local bundle, including an MCP export. They
 also accept portable inline Evidence and use the same application workflows.
 A standalone CLI invocation cannot resolve another MCP connection's ledger
-without that exported bundle. See [CLI Evidence reuse](../getting-started/cli.md#import-export-and-compare-evidence)
+without that exported bundle. See [CLI Evidence reuse](cli.md#import-export-and-compare-evidence)
 for the supported commands. No additional lookup call, provider selection, or
 approval step is required for a same-session follow-up.
 CLI `inspect-artifact` continues to return complete portable Evidence. Save that
@@ -948,20 +842,13 @@ parent for another invocation.

 ## Identity and discovery

-When an admitted `open_binary` attempt fails, its error details include
-`target_at_open_completion`: the selected binary target when that attempt
-settled, or `null` when none was selected. `provider_id_at_open_completion`
-names its bound deep provider, or `null` if none was bound. A later lifecycle
-operation can change either selection; call `binary_session` for current state. This field does
-not establish provider readiness or resource cleanup.
-
 `binary_session` reports the active package, server, SDK, and negotiated
 protocol details. `rea doctor` separately inspects supported JSON/TOML client
 registrations, reports their command vectors as aligned, stale, missing, or
 invalid, and keeps live-server state `unknown` unless the active connection
 supplies identity.

-By default, `tools/list` returns the complete canonical tool inventory, including tools that
+`tools/list` returns the complete canonical tool inventory, including tools that
 are currently unavailable. Opening or closing a target or observing a provider
 health transition leaves that catalog unchanged and does not emit
 `notifications/tools/list_changed`.
@@ -973,7 +860,7 @@ share status facts. `tool_availability.client_requirements` is the baseline for
 each group; a group's optional `client_requirements` replaces that baseline for
 the group's tools. Expand each group's `names` into one tool entry, carrying its
 availability, reason, remediation, default-mode status, modes, and client
-requirements. With the default full catalog, compare the union of group names with `tools/list` when checking
+requirements. Compare the union of group names with `tools/list` when checking
 that a client received the full catalog. An operation absent from all groups is
 missing from the complete inventory; it is not an implicit unavailable entry.

@@ -1014,18 +901,6 @@ finish without reading relationships, even when neither traversal mode is
 available. Discovery does not block that direct invocation or replace its typed
 partial/error outcomes.

-`trace_native_values` includes `value_flow_support` for the provider routed to
-`analyze_function`. `supported` declares that the provider may supply value flow;
-it does not guarantee a model for the selected function. `unavailable` includes
-the provider's reason, and `unknown` means no declaration. The provider ID is
-preserved, or null if no analysis provider is routed. This declaration is separate
-from operation readiness and the availability of call-target resolution. When
-call-target resolution is missing, a direct trace may still return a local graph
-with call-resolution unknowns; even `max_depth: 0` attempts to resolve call sites.
-When support is unknown but the declared operation prerequisites are ready,
-availability can still be true; it does not promise that value flow is present.
-The trace's returned observations and unknowns remain authoritative for that call.
-
 `trace_native_ui_action` reports authored-UI and native-seed modes separately.
 Apple dispatch metadata requires a Mach-O target; another provider may supply
 the symbol-only alternative on other formats. If neither mode is available,
@@ -1079,28 +954,7 @@ analysis client. `open_binary.provider_id` accepts a concrete provider ID or
 concrete version, selection source, and complete analysis profile through
 `analysis_provider_binding`. Ambiguity and unknown, unavailable, or unsupported
 choices return typed selection details. A selected provider is never replaced
-automatically after a runtime failure. When the bound route does not declare an
-operation, its error points to `binary_session` with `detail: "complete"` for
-candidate capabilities and an explicit `open_binary` provider choice. A
-candidate's availability does not guarantee support for the selected target;
-switching may discard provider session edits, and retained Evidence does not restore them.
-
-When the selected provider reports `release_verification` in its binding,
-the status compares its reported release version at binding with the provider's
-verified baseline. It does not recheck the executable, authenticate its bytes,
-or guarantee results.
-An unverified release may still be usable; the optional remediation preserves
-the caller's choice. Omission means verification was not reported. Target-free
-discovery does not probe a version solely to populate this fact.
-
-When an admitted `open_binary` attempt fails, `error.details.selection_at_failure`
-records the canonical binary path and SHA-256, resource root (including its
-caller-selected path), or absence of selection at
-the end of that serialized attempt. This is a past observation: a queued or
-later operation may already have changed the selection. No selection does not
-establish that cleanup is complete. Call `binary_session` for current state
-and cleanup status. Validation failures that do not enter the session have no
-such receipt. The original error and any cleanup recovery remain authoritative.
+automatically after a runtime failure.

 `open_binary` resolves an Apple bundle directory (`.app`, `.appex`,
 `.framework`, `.xpc`, `.systemextension`, `.bundle` or `.plugin`, compared
@@ -1362,22 +1216,6 @@ Those raw observations are not recorded in the Evidence bundle. If the SDK
 suppresses the error reply after client cancellation, Evidence tools cannot
 recover them. An empty bundle does not prove that no partial work or side
 effect occurred; output receipts and cleanup observations remain distinct.
-If an authenticated Evidence record exceeds the investigation's retention
-allowance, the refusal carries it inline as
-`details.partial_observation: {kind: "unretained-evidence", evidence: ...}`
-when it fits the response budget. Its ID identifies the supplied content; it
-is not a retained-session reference. If authentication itself failed or lacked
-headroom, no authenticated Evidence is claimed. When the completed record does
-not fit the MCP response, the original retention error carries
-`details.partial_observation_omitted` with the response constraint if the
-remaining error fits; the observation remains unretained. Otherwise the usual
-oversized-error recovery applies.
-When an atomic derived-Evidence and Unknown write exceeds the allowance after
-authentication, the completed Evidence is returned the same way if absent from
-the investigation. If that exact Evidence was already present, the error
-instead carries `{kind: "retained-evidence", evidence_id: ...}` for the current
-session. The refused write adds neither a record nor an Unknown revision; a
-previously retained record or Unknown remains available.
 The broader retention decision is tracked in
 [#4276](https://github.com/morluto/rea/issues/4276).

@@ -1497,11 +1335,11 @@ failing owner supports runtime recovery; `inspect_analysis_settings` is optional
 when those facts are supplied. Updates are atomic, apply to new work, survive
 target close/open, and vanish when REA exits. Explicit per-call arguments take
 precedence. Neither tool changes host deadlines or resolves retained cleanup.
-See [runtime settings and recovery](../design/limits-and-recovery.md#runtime-settings-through-mcp)
+See [runtime settings and recovery](design/limits-and-recovery.md#runtime-settings-through-mcp)
 for the full setting list, reset/revision semantics and ASAR retry example.
 For implementation ownership, accepted-operation snapshots, provider wiring,
 and extension guidance, see the
-[maintainer design](../design/limits-and-recovery.md#ownership-and-data-flow).
+[maintainer design](design/limits-and-recovery.md#ownership-and-data-flow).

 Ghidra and Hopper startup updates apply to the next startup attempt without
 restarting REA. Ghidra decompile timeout updates apply on the existing Program.
@@ -1515,7 +1353,7 @@ that Ghidra has finished importing the target. The first Ghidra-backed query,
 such as `binary_overview`, starts the engine and waits for import, default
 auto-analysis, bridge connection, and health readiness before returning analysis.
 With `REA_GHIDRA_PROJECT_PATH`, shared CLI/MCP configuration instead selects an
-[existing project copy](../getting-started/installation.md#reuse-an-existing-ghidra-project), whose
+[existing project copy](installation.md#reuse-an-existing-ghidra-project), whose
 content fingerprint is committed into the profile. Import, auto-analysis and
 repair scripts are skipped; original analysis completeness/settings stay unknown,
 and bridge database edits are unavailable. The same startup/client deadlines
@@ -1531,7 +1369,7 @@ These deadlines have different owners:
 | Darwin swiftc helper | REA allows 120,000 ms by default for ownership-helper compilation; `REA_SWIFTC_COMPILE_TIMEOUT_MS` accepts decimal integers from 1–2,147,483,647 ms. Invalid values fail configuration validation. Set it in the environment that starts REA and restart REA; the next ownership-helper compile uses the new value. |
 | Individual tool call | The client bounds its wait, including cold engine startup. The pinned client SDK 2.3.1 defaults to 60,000 ms and can cancel earlier than REA's startup deadline.                                                                                                                                                    |

-For [Codex and Kimi registrations](../getting-started/client-configuration.md), setup supplies
+For [Codex and Kimi registrations](client-configuration.md), setup supplies
 missing tool deadlines from the known provider allowance plus 120 seconds of
 operation headroom: 450 seconds with the default Ghidra allowance, or 2820
 seconds with `REA_GHIDRA_STARTUP_TIMEOUT_MS=2700000`. Positive caller-selected
@@ -1621,7 +1459,7 @@ clear cleanup blockers, or extend the client's deadline. Alternatively, change
 `REA_GHIDRA_STARTUP_TIMEOUT_MS` in REA's launch environment and restart the
 server, preserving Evidence and closing as above. Close/reopen on the same
 connection cannot apply a changed launch environment. See the
-[CLI retry example](../getting-started/installation.md#ghidra).
+[CLI retry example](installation.md#ghidra).

 This close/reopen flow was exercised on one real Linux stdio connection after a
 controlled startup timeout, followed by a successful overview and function
@@ -1659,21 +1497,12 @@ cursor outside a procedure is represented as
 procedure resolution returns typed unreadable output; provider errors never
 become absence from their message text. `inspect_address_context` requires an explicit address and
 returns name, procedure, comment, inline-comment, and bookmark facets;
-unsupported facets are local `unavailable` outcomes. A facet rejected for
-invalid input or a resource constraint includes its canonical `error`
-projection, including structured issues or reported limits and recovery,
-alongside the other facet outcomes. Use `current_document`,
+unsupported facets are local `unavailable` outcomes. A facet whose input is
+rejected includes its canonical `error` projection, including any structured
+issues, alongside the other facet outcomes. Use `current_document`,
 `current_address`, and `current_procedure` for direct single-field lookups; use
 the aggregate tools when you need related context together.

-If unretained facet Evidence makes the context response exceed an MCP delivery
-limit, REA omits those partial records in estimated size order until the reply
-fits. Each affected facet identifies its unretained omission and the delivery
-constraint; other facets and partials remain in the response when they fit. The
-size estimate is used only for ordering and can omit more records than a perfect
-wire-size ordering would. If the remaining context still cannot fit, call the
-needed address operations individually and follow their delivery diagnostics.
-
 ## Integrity attribution and reconstruction claims

 Artifact comparison results include `integrity_mismatch_evidence_ids`, naming
@@ -1710,26 +1539,6 @@ canonical `integrity_contradictions` records and marks application graph
 coverage partial when any mismatch is continued. Contradicted nested ASARs
 remain opaque.

-`extract_artifact` accepts optional `output_root` and `occurrence_ids` inputs.
-The CLI equivalents are `--output-root` and repeatable `--occurrence-id`.
-`output_root` is an absolute path on the REA host: its parent must exist and the
-root must not exist, even as an empty directory or a symbolic link. Omitting it
-keeps the fresh `rea-extracted-<uuid>` directory under Node's temporary directory
-(`TMPDIR` on POSIX). Successful output persists after the call and client close;
-the caller owns its later removal. A failed extraction rolls back only its own
-output and reports any cleanup failure.
-An output root inside the source directory, including a symlink alias, is refused.
-
-Obtain exact IDs from the active artifact's inventory. Omitting `occurrence_ids`
-extracts all regular entries exposed by the active reader. An explicit selection
-must be nonempty and unique; unknown IDs, directories, links, the root and nested
-archive members are rejected before output creation. Open the containing archive
-separately to extract its nested members. Selection is by occurrence, not content
-hash, so equal bytes at different paths remain independently selectable. Only
-selected files face destination name collisions; input path and integrity checks
-still cover the full inventory. The extraction manifest records exactly which
-occurrences were materialized and retains the source manifest identity.
-
 `extract_artifact` accepts the same policy in MCP and as `--integrity-policy`
 on `rea extract-artifact`. With `record-and-continue` it writes the observed
 bytes and returns the `integrity_contradictions` records for the extracted
@@ -1765,49 +1574,6 @@ support for omitted historical values.
 known and differ. If only one value is known, storage comparison is unknown;
 when both are omitted, storage is not compared.

-<!-- BEGIN:compare-artifacts:compared-format-metadata-kinds -->
-
-`compare_artifacts` also compares the declarations in the `format_metadata`
-of UnityFS members (`unityfs-entry`), PyInstaller entries
-(`pyinstaller-entry`), Node SEA members (`node-sea-entry`),
-ESP image segments (`esp-image-segment`), DfuSe elements (`dfuse-element`),
-ESP flash partitions (`esp-flash-partition`) and FIT images (`fit-image`);
-each format's guide names the compared fields. A changed declaration is a
-metadata change, including when content is unavailable. A declaration that
-only one side records, or that the other side records as another kind, is
-unknown and adds a limitation. A field that either side could not read is
-unknown, and the other fields still compare. Other kinds are not compared:
-their fields record layout, come from the bytes of the artifact or its
-container or from caller options that identify the target, or repeat
-occurrence fields, except Godot PCK source paths, which
-[Godot PCK archives](../godot-pck.md) explains.
-
-<!-- END:compare-artifacts:compared-format-metadata-kinds -->
-
-Every occurrence records `entry_kind`, `executable` and `encrypted`. A
-different entry kind, `encrypted` value or occurrence limitation text is a
-`metadata` difference, and a different `executable` value is an `executable`
-difference. A symlink's own permission bits never mark it `executable`,
-because running a symlink runs its target. When either side's content is
-unavailable, `compare_artifacts` lists the differences that it can still
-observe with `availability`, and the path compares `unknown` unless a
-declaration changed. REA does not read symlink targets or encrypted bytes,
-so a non-executable file that becomes a symlink compares `unknown` in
-`metadata` and `availability`, and so does a member that becomes encrypted.
-Declared sizes do not count without content: REA compares observed sizes.
-For a node-less metadata record with a compared declaration, only that
-declaration, these fields and any recorded ASAR storage decide the
-comparison, so a record that becomes encrypted compares `changed` in
-`metadata`. Such a record adds `availability` only when a declaration is
-unknown. REA does not compare the record's unread payload or its
-limitations, which describe the observation.
-
-When either side has no content, `compare_artifacts` also compares the
-occurrences' `declared_integrity` claims, which Godot PCK and ASAR readers
-record. Claims of one algorithm that differ add `metadata`. REA cannot verify
-them, so they do not make the path `changed`, and equal claims add nothing.
-With content on both sides, the observed bytes decide.
-
 POSIX letter-colon names such as `a:b` remain valid logical
 names; Windows extraction refuses names its filesystem cannot materialize.

@@ -1951,9 +1717,7 @@ JSON Schema:

 - Annotation prose leaves the advertised form: nested property descriptions,
  literal examples, defaults, and titles are dropped. The root keeps its
-  description because it states the accepted input groups. A root `detail`
-  property keeps its description because it selects between complete Evidence
-  and a bounded summary.
+  description because it states the accepted input groups.
 - Schema-local references are inlined within the budget. Kimi Code expands
  references before sending provider requests, so sharing definitions cannot
  establish the provider-facing size. Expansion stops at the budget before
@@ -1984,55 +1748,6 @@ check full-profile local-path rules. Compact MCP workflow tests verify canonical
 rejection of invalid inputs before provider work, independent of how much detail
 the selected advertisement retains.

-<a id="hotcold-catalog-discovery"></a>
-
-### Hot/cold catalog discovery
-
-`REA_MCP_TOOL_CATALOG_PROFILE=hot-cold` opts into per-connection loading for
-clients that refresh `tools/list` after `notifications/tools/list_changed`.
-The default, `full`, retains the complete upfront advertisement. Restart the
-server to change profiles. See [client configuration](../getting-started/client-configuration.md#hotcold-catalogs).
-
-Hot/cold initially advertises `binary_session`, `open_binary`, `close_binary`,
-`get_evidence_bundle`, and the adapter's `discover_tools`.
-`inspect_analysis_view` is loaded on demand like other analysis tools. When a
-follow-up needs retained facts, include it in `discover_tools.names`; if the
-producer and follow-up are known together, load both in one batch. Producers
-that accept `view` can answer a selected first question without loading the
-cross-domain view contract. Complete output schemas and canonical result
-validation are preserved when each tool loads.
-An explicit tool-family scope can remove any of those domain tools.
-`discover_tools` searches canonical names and descriptions using case-insensitive
-words, or accepts exact `names`. It loads the matching page and returns names
-and abbreviated descriptions with their configured input schemas, so the next
-call can use the returned arguments contract. Output schemas remain in
-`tools/list`. Search defaults to three results, allows up to
-20 per page, and returns `total_matches` and `next_offset`. Exact names preserve
-request order and reject unknown or excluded names before loading anything.
-Use fewer keywords when no result matches; search requires every word to match.
-Both reply representations must fit the configured response budget before any
-tools load. An oversized page returns a resource constraint; reduce `limit` or
-request fewer exact names and retry. Input schemas are retained in full within
-the selected input profile.
-
-Loaded definitions retain their original names, complete configured schemas,
-annotations, handlers and client approval rules. Loading does not execute an
-analysis, open a target, or initialize the deferred analysis runtime. A batch
-emits one list-change notification; repeating it emits none. Loaded tools remain
-available until the connection ends. There is no generic execution gateway.
-If a loaded tool does not appear in the client, enable client catalog refresh
-or reconnect using `REA_MCP_TOOL_CATALOG_PROFILE=full`.
-
-The catalog identity covers the complete in-scope inventory, the discovery
-contract and the hot/cold policy; its count includes `discover_tools`. It differs
-from full advertisement and remains stable as tools load. `rea mcp doctor`
-checks the profile's initial advertisement and identity. The domain inventory in
-`binary_session.tool_availability` continues to describe provider and target
-availability, independently of whether a definition is loaded. Load a listed
-cold tool before calling it. Provider health and target changes do not load,
-unload or remove definitions. The input/output schema profiles and explicit
-family exclusions continue to apply.
-
 ### Tool family advertising scope

 Agents pay context for every advertised tool schema, and clients that send
@@ -2094,7 +1809,6 @@ bundle import/export; it does not include those view and settings tools.
 | Web investigation                                 | `browser,pcap,session,javascript-runtime`                 | page, bundle and session inspection, packet captures, JS runtime observation, evidence workflow                                                              |
 | Android application analysis                      | `android,adb,apktool,session`                             | class and method inspection, device bridge, resource decoding; add `frida` for dynamic instrumentation, `jeb` for JEB projects, `flutter` for Flutter builds |
 | Native macOS or iOS binary                        | `native,artifact,session`                                 | Mach-O, signature and property-list inspection plus container extraction                                                                                     |
-| Native analysis of a known function               | `session,enhanced,application`                            | open a binary, analyze a known function, page retained pseudocode, and export Evidence; add `direct` for focused procedure search or assembly                |
 | Managed .NET assembly                             | `managed,session`                                         | managed member comparison and reconstruction against the evidence workflow                                                                                   |
 | Electron or browser-hosted JavaScript application | `browser,electron,application,javascript-runtime,session` | runtime targets, live page inspection, bundle and capture tools, feature tracing, JavaScript semantics and reconstruction obligations                        |
 | Evidence bookkeeping only                         | `session`                                                 | open and close binaries, bundles, comparisons, unknown tracking                                                                                              |
@@ -2120,20 +1834,15 @@ profile and the advertised form that profile produces. `full`, `compact`, and
 bounded schemas clients receive; `off` keeps the canonical output contracts in
 the digest while advertising nothing.

-Some clients reject a complete `tools/list` frame or HTTP SSE event before
-they load any tools. The opt-in `REA_MCP_OUTPUT_SCHEMA_PROFILE=compact`
-setting bounds every advertised output schema to 4,096 bytes; `off` omits `outputSchema` entirely
+Some stdio hosts reject a complete `tools/list` frame before they load any
+tools. The opt-in `REA_MCP_OUTPUT_SCHEMA_PROFILE=compact` setting bounds every
+advertised output schema to 4,096 bytes; `off` omits `outputSchema` entirely
 (the measured pi-web-ui failure and catalog breakdown are in
 [#2512](https://github.com/morluto/rea/issues/2512)). The default `full` profile
 is unchanged. Both settings keep the same named canonical tool contract for
 server-side result validation, and both still return complete
 `structuredContent` and text results.

-For the 1 MiB FastMCP SSE limit reported by Unsloth in
-[#9093](https://github.com/morluto/rea/issues/9093), see the
-[tested catalog configuration](../getting-started/client-configuration.md#fastmcp-and-unsloth-sse-catalog-limits).
-Hot/cold selection alone does not bound later catalog refreshes.
-
 `compact` keeps the complete validation structure when it fits the budget.
 Otherwise it advertises the root property shape, first-level reference-resolved
 types, first-level guidance, and the root's `required`/`additionalProperties`
@@ -2230,27 +1939,18 @@ establish an observed difference against a complete peer, but an omitted request
 does not establish removal. Partial WebSocket streams do not establish frame
 alignment. WebMCP frame IDs and tool keys are local to a capture; semantic owner
 facts and known counts determine correspondence. Retained script digests can
-establish source changes. See [browser comparison semantics](../guides/web/browser-observation.md)
+establish source changes. See [browser comparison semantics](browser-observation.md)
 for value uncertainty and storage-fingerprint recapture requirements.

 ## Generated catalog

 Custom clients upgrading from 6.1 should follow the
-[6.2 migration guide](../migrations/migration-6.2.md#mcp-results-and-evidence).
+[6.2 migration guide](migration-6.2.md#mcp-results-and-evidence).

 Run `npm run docs:generate` in a source checkout to generate the machine-readable
 catalog at `docs/public/product-catalog.json`. Documentation deployments serve
-the same file at [/rea/product-catalog.json](../public/product-catalog.json). PR CI retains it with the packaged
+the same file at [/rea/product-catalog.json](/rea/product-catalog.json). PR CI retains it with the packaged
 skill and portable conformance projections in the `generated-docs` artifact.
 These outputs describe the exact source revision being built; they are not
 checked-in snapshots. For a running server, `binary_session` remains the
 authoritative source of catalog identity and tool availability.
-
-## Offline Playwright traces
-
-`inspect_playwright_trace` reads a local v10 trace ZIP and defaults to a retained
-summary. `playwright-trace` views select source-located action boundaries, console
-and network facts, resource references and diagnostics; long text has bounded
-previews and character pages. Import does not contact recorded URLs or use a
-browser. See [offline Playwright traces](../playwright-traces.md) for coverage,
-resource policies and the shared CLI workflow.
@@ -61,18 +61,12 @@ locator unreadable.
 | `audit_residual_unknowns`         | Audit current residual-unknown heads and evidence-qualified resolution.              |
 | `prepare_bounded_process_capture` | Design a bounded controlled process experiment before execution.                     |

-A `REA_MCP_TOOL_FAMILIES` scope advertises a workflow when its required tools
-belong to selected families. Optional APK, managed, Apple-resource, and archive
-routes in `investigate_feature` are omitted when their tools are disabled;
-they do not make the existing native and JavaScript workflow unavailable.
-Apple plist guidance requires both the session opener and the native plist
-reader. Interface Builder, asset catalog, and keyed archive guidance requires
-the opener and the artifact readers. An opener alone never advertises an Apple
-resource route; opening resources switches away from the active binary session.
-Workflows missing a required tool are omitted from `prompts/list`, and
-`prompts/get` reports them as not found. Rendering, the server identity digest,
-and `rea mcp doctor` use the same scoped contracts, so guidance never directs
-the agent to a disabled call.
+A `REA_MCP_TOOL_FAMILIES` scope advertises a workflow only when every tool in
+its suggested steps belongs to a selected family. Partially available
+workflows are omitted from `prompts/list` — `prompts/get` reports them as not
+found — so a rendered prompt never directs the agent to a disabled call. The
+server identity digest and `rea mcp doctor` prompt inventory follow the same
+scope.

 Every rendered prompt provides optional starting points using current REA tool
 names. Agents can call tools directly, skip irrelevant suggestions, and inspect
@@ -38,7 +38,7 @@ if (reply.isError === true) {

 Lifecycle and other non-Evidence tools still use their own advertised output
 contracts. Do not assume every successful tool returns Evidence. Consult
-[`tools/list` and the result guide](../reference/mcp-contracts.md#tool-results).
+[`tools/list` and the result guide](mcp-contracts.md#tool-results).

 A transport `resource_constraint` error can include a retained
 `details.reported_limits.evidence_reference`. Use `inspect_analysis_view` or
@@ -79,7 +79,7 @@ rea analyze /absolute/path/to/program --provider ghidra --snapshot /absolute/pat
 In MCP, open the target without the incompatible `snapshot_path`, run the
 required queries, then save to a new path through `close_binary.snapshot_path`.
 Do not fabricate missing provider profiles or query bindings. See
-[snapshot usage](../getting-started/cli.md#save-and-reuse-analysis-snapshots).
+[snapshot usage](cli.md#save-and-reuse-analysis-snapshots).

 Artifact inventory nodes identify content bytes. Path-specific role and
 permissions now belong to each occurrence:
@@ -46,18 +46,6 @@ fingerprint and the same known architecture. Extents are never guessed from the
 next entry, and relocations are not normalized. A larger mapped read can serve
 several observed bodies; only needed ranges need to be captured.

-For a matched function, its `evidence_links` include the selected byte reads
-that covered its body. Request the `function-matches` view with
-`collection: "byte-sources"` to page the selected `read_bytes` source IDs,
-sides and limitations; intersect those IDs with the function's links. This
-distinguishes, for example, Ghidra initialized-memory bytes from file bytes.
-Identical overlapping reads retain the selected covering source, not every
-corroborating read. Pages preserve the original source limitations and may end
-early when the response budget is reached. If one source is too large for a
-page, the error identifies its Evidence and the next offset; inspect the
-original matching Evidence or export it if retained, then resume at that
-offset. Older matching Evidence may not record this source selection.
-
 This first slice reuses existing range observations. Stripped builds can require
 many lightweight range queries when those facts are not retained yet. Matching
 does not hide that acquisition cost or silently start those queries. Full
@@ -95,8 +83,7 @@ counts, both identities and coverage. Query its `parent_evidence_id`:
 counts. Large member lists are omitted by default; select `left`/`right` columns
 explicitly or page individual `functions`. Batch `match_ids`/`function_ids`, exact function `names`, state
 and side filters intersect. Mandatory identities and provenance survive column
-selection. Default function rows include member limitations; an explicit `fields`
-selection can omit them. Page coverage covers selected retained facts. Function identity binds
+selection. Page coverage covers selected retained facts. Function identity binds
 inventory Evidence and the owning inventory’s `source_index`, preserving same-address alternatives.
 One validation, lazy member index and bounded recent filter are retained per
 immutable parent; no live target state is cached.
@@ -21,7 +21,7 @@ breakpoint names.

 ## Start with a function

-Choose an installed provider from [setup](../../getting-started/installation.md#hopper). For Ghidra:
+Choose an installed provider from [setup](installation.md#hopper). For Ghidra:

 ```bash
 rea inspect /absolute/path/to/program --provider ghidra --json
@@ -43,17 +43,6 @@ focused tools such as `list_procedures` and `analyze_function` on the same sessi
 | What did the declared runtime scenario observe?              | [Desktop](#native-desktop-observation) or [call observation](#native-call-observation) |
 | What can this provider and host establish?                   | [Provider boundaries](#provider-and-verification-boundaries)                           |

-For large pseudocode, request `procedure_pseudo_code` with `detail: "summary"`
-on the first MCP call. It retains the complete observation and returns the
-original selection, text availability and length without the body. Use
-`normalized_result.parent_evidence_id` with `inspect_analysis_view` and
-`view: {kind: "native", facet: "pseudocode", offset: 0, limit: 20000}`;
-follow `coverage.next_offset` for later pages. Offsets and limits count UTF-16
-code units, not lines or tokens. Pages reuse the same observation without
-repeating decompilation. Null and empty text remain distinct. Omitted or
-`complete` detail preserves full inline delivery. Summary delivery requires a
-retaining session and does not reduce the work or memory of decompilation.
-
 ## Exact CLI selectors

 `function`, `instructions` and `decompile` accept `--procedure=<name-or-address>`;
@@ -83,9 +72,6 @@ its address when selecting the containing function. `search_procedures` matches
 the same names, in leaf or qualified spelling: the function appears once with
 its primary name as `value`, and `matched_aliases` lists the qualified names of
 the secondary symbols that matched.
-For Ghidra case-insensitive literal searches of procedures or strings,
-`raw_result` contains bridge candidates before REA applies Unicode-aware
-matching. Use `normalized_result` for matches; a raw candidate need not match.
 Overloads can share a fully qualified name; ambiguity errors return every
 matching entry address so the caller can select the intended function directly.

@@ -142,16 +128,6 @@ rea inspect-native-data-type <binary> --type /MyStruct --provider ghidra
 rea inspect-native-data-type <binary> --address <typed-data-address> --provider ghidra
 ```

-Ghidra bit-field components may have a `type_id` that is not a registered
-database type. When `bit_field` is present, `base_type_id` is the provider's
-base type and the lookup fields report whether the manager resolves equivalent
-types at those exact paths. `bit_size` is the effective width;
-`declared_bit_size` can be larger. `bit_offset` is the least-significant-bit
-offset within the base type, not a byte-order-independent offset from the start
-of the containing structure. Account for the component's storage size and byte
-order before applying that offset to a larger word. Missing `bit_field` details
-are unreported, not proof that a component is not a bit-field.
-
 Instruction facts include bytes, length, decoder text, ordered register/scalar/
 address tokens, typed references and flow destinations. Mid-instruction, data,
 outside-memory and unlisted addresses have separate outcomes. For Ghidra,
@@ -228,7 +204,7 @@ single-procedure CLI operation.
 `detail: "summary"` retains the complete batch and returns only its counts,
 identities and sizes. `inspect_analysis_view` then reads rows or one body from
 the retained record, an Evidence file or a portable bundle without repeating
-decompilation: see [selected batch results](../../reference/mcp-contracts.md#selected-batch-decompile-results).
+decompilation: see [selected batch results](mcp-contracts.md#selected-batch-decompile-results).

 Each batch schedules one provider read at a time, but has no shared input-count
 or aggregate retained-output allowance. It retains every requested row and full
@@ -250,33 +226,8 @@ the index retains the complete selected names, addresses, provider facts and
 caveats. Failure details retain at most 32 rows within 2,048 JSON-encoded
 UTF-8 bytes; names may be omitted to keep complete addresses and reasons. The
 index retains every failure and its complete observed name.
-The manifest reports the procedure-inventory limitations of the current call in
-`inventory_limitations`. `decompile-index.json`'s `latest_run` records that
-call's filters, selected and excluded counts, and inventory limitations; older
-runs remain represented only by their retained function records, so a later
-inventory warning is not presented as the history of every file.
-Use `retry_failed: "independent_fresh"` (CLI: `--retry-failed independent_fresh`)
-to request an independent attempt after a null pseudocode observation that the
-provider explicitly reports as a function failure. The failed observation is
-appended before the retry, so cancellation or a later failure keeps it. The
-retry can use different analysis context. Other errors and entries merely
-missing from an export are not retried. A null without a reported function
-failure carries a limitation explaining why no independent retry was attempted.
-A provider that does not report this distinction leaves the cause unknown.
 Each function's `decompile-index.json` record, whatever its status, keeps the
-complete limitations of the observations it used. The index keeps the latest
-record for each function; `decompile-journal.jsonl` keeps earlier attempts and
-their separate limitations.
-When available, `provider_source` records the source of that attempt's
-pseudocode observation: a file path, SHA-256 and byte range, or a
-single-function decompile. The latter describes the method, not a unique run. A file
-descriptor records the source as observed; the file may since have changed or
-been removed, so compare its current digest before using it. The descriptor
-does not authenticate the journal. `status: "unknown"` distinguishes
-an unavailable source from an existing matching output whose original producer
-is unknown. Older journal records can omit this field; omission is unknown.
-Failed attempts retain their source in the append-only journal when the
-provider supplied one, even if a later attempt succeeds. The returned Evidence keeps
+complete limitations of the observations it used. The returned Evidence keeps
 at most eight first-observed distinct per-function provider limitations within an 8,000-byte JSON-encoded UTF-8 text budget and counts omitted observations. Repeated omitted text is counted per observation, not as a distinct caveat. This summary does not retain every omitted string in memory. A fresh output directory must not already exist. `--resume`
 continues an export for the same target SHA-256, provider, analysis profile,
 and layout; it requires the directory to exist, and an export without a known
@@ -383,7 +334,7 @@ configuration errors and do not fall back to 128. The setting is read from
 the environment that starts REA, while MCP `regex.worker_heap_request_mib`
 can override it for workers belonging to newly accepted searches. Use
 `update_analysis_settings` for either runtime control; accepted work keeps its
-budget. See the [settings design](../../design/limits-and-recovery.md).
+budget. See the [settings design](design/limits-and-recovery.md).
 A heap failure names the effective request, known source, default, floor, and
 maximum. A positive Node.js
 `--max-old-space-size` on the process that starts
@@ -497,18 +448,6 @@ nodes and edges. Node payloads are bounded to 8 MiB and serialized results to
 32 MiB. Pagination returns edges whose source is on the node page and preserves
 stable IDs for endpoints outside that page.

-Procedure, node and edge `evidence_id` values identify the source function
-observations used by the trace. In an MCP session, retrieve them from the
-Evidence bundle for inspection or export. A replayed source keeps the original
-observation's identity; the trace also reports that replay occurred. Older
-cached value traces are not replayed under the revised workflow profile, while
-their historical Evidence remains available.
-
-The one-shot CLI accepts `--evidence_output <new-path>` to save the trace and
-the transitive source Evidence closure named by its links. The destination is
-never overwritten. `--detail summary` requires `--evidence_output`; the bundle
-still retains the complete trace and source Evidence.
-
 Within one value trace, each exact procedure selector is attempted at most once,
 including failed analyses. A failed seed returns the provider's original typed
 failure and corrective guidance; it cannot establish a trace or target identity.
@@ -519,10 +458,8 @@ resources it owns stops the trace: the result is that provider's own
 `cleanup_incomplete` failure with its resources and any bound cleanup retry, and the work
 admitted before the stop is retained as partial Evidence with a located unknown
 at the stopping read. A successful seed without a native def-use
-model still returns its procedure and an explicit coverage unknown. An unrecorded
-facet stays unknown; when the provider explicitly reports unavailability, the trace
-retains its reason. REA's Kuna provider explicitly reports that it does not supply
-native def-use observations. A new trace can retry failed selectors.
+model still returns its procedure and an explicit coverage unknown. A new trace
+can retry failed selectors.

 Paging and traversal completeness are separate facts. `page_truncated` means the
 page omits retained nodes, and the edges they source, before `offset` or after
@@ -544,17 +481,8 @@ The raw Java `is_dead` flag can remain set after Ghidra decodes a live block;
 `block_membership` reports actual syntax-tree membership separately.

 The provider dossier itself retains up to 3,000 p-code operations, 64 inputs per
-operation and 12,000 def-use edges, with explicit omitted counts. Memory effects
-cover high-p-code `LOAD` and `STORE` operations; direct memory address varnodes
-in other operations are excluded, so an empty effect list does not establish
-that the function accesses no memory. `procedure_references` can supply
-complementary recorded instruction references, with its own coverage limits. A
-`STORE` may describe stack memory and does not itself prove persistent state.
-The Ghidra analysis profile commits to this effect scope. Snapshots from before
-that commitment are rejected; analyze without the snapshot and save a fresh one.
-To keep historical Evidence, copy the old snapshot's `evidence_bundle` object to
-a separate JSON file and import that bundle. Import validates the Evidence; it
-does not replay the old provider analysis.
+operation and 12,000 def-use edges, with explicit omitted counts. A `STORE`
+may describe stack memory and does not itself prove persistent state.

 Jump-table evidence keeps numeric `mappings`, explicit `default_targets`, and
 backing `data_sources` separate. A null case value denotes an unresolved
@@ -779,7 +707,7 @@ complete observation.
  It reports each `@rpath`, `@loader_path` and `@executable_path` candidate with
  its outcome. Paths outside the analyzed root, including shared-cache system
  libraries, stay undetermined. See
-  [Apple application analysis](../apple/apple-application-analysis.md#dylib-load-resolution).
+  [Apple application analysis](apple-application-analysis.md#dylib-load-resolution).
  ARM64 slice labels distinguish `arm64v8`, `arm64e`, and `arm64e.x1` while
  retaining raw CPU subtype and capability bits. The `arm64` and `arm64e`
  request filters select their respective families; a shared family label
@@ -949,13 +877,6 @@ complete observation.
  section lengths and unsupported non-PowerPC big-endian CPU declarations return
  `unsupported_target` with the selected path and precise reason. Recovery
  selects a well-formed or supported artifact and reopens that target.
-  An unreadable adopted-protocol sublist leaves its class, category or
-  `objc_protocol_records` entry available with partial decode status and
-  `protocol_list_unreadable`. Independently decoded metadata and any readable
-  protocol-name prefix remain available; an empty partial list does not
-  establish that its owner adopts no protocols. Existing list and record
-  limits remain in effect. Reader v3 uses a new analysis profile; snapshots
-  bound to reader v2 are incompatible and must be regenerated for this recovery.
  The byte reader holds the whole selected file in memory, so it admits files up
  to 64 MiB / 67108864 bytes by default. Select a larger budget with
  `max_input_bytes` (CLI `--max-input-bytes`), at most 1 GiB / 1073741824
@@ -1176,25 +1097,6 @@ arguments. The receiver class comes from LLDB's Objective-C runtime reader
 without running target code; no expression is evaluated, and REA never
 attaches to a process it did not launch.

-Resolved breakpoint locations, entries and caller frames also retain
-`source_location` from LLDB's line tables when available. Its `file_path`,
-one-based `line` and one-based `column` are independently nullable. An invalid
-line entry is null; historical captures may omit the field. This is debug metadata
-attribution: REA does not read that source path or verify the source file bytes.
-Absent coordinates do not imply that the executable has no source code.
-
-Free Pascal programs with retained native symbols and usable DWARF can use this
-same bounded call observation on macOS. Select an exact emitted symbol from the
-binary rather than assuming a source procedure name. The owned Pascal fixture
-uses an explicit C calling convention and a public symbol; its verification
-covers call entries, raw integer registers and source coordinates, without
-establishing typed Pascal locals or interactive stepping. After building REA,
-run the real lane with an existing caller-selected compiler:
-
-```sh
-REA_VERIFY_FPC_COMMAND=/absolute/path/to/fpc npm run verify:native:pascal-calls
-```
-
 The run ends when the process exits, `max_events` entries are recorded,
 `duration_ms` elapses, or the aggregate trace resource budget is exhausted.
 Bounded termination reports partial coverage. REA checks process termination
@@ -1259,18 +1161,15 @@ is present. A denied trace reports the `debugger-attach-denied` reason.
 Install a Ghidra 12.x (>=12.1) release and the 64-bit full JDK it declares, then configure REA to
 use them. Ghidra analysis supports Linux x64/arm64 and macOS x64/arm64; each installation requires
 the matching native decompiler. Experimental Windows x64 P0 admits native
-x86, x86-64, ARMNT (Thumb-2) and ARM64 PE applications and DLLs, [DOS MZ
-executables](../../providers/ghidra-dos.md), plus explicitly selected
-[raw NMOS 6502 images](../../providers/raw-binary.md#nmos-6502) with a caller-supplied load address,
+x86, x86-64, ARMNT (Thumb-2) and ARM64 PE applications and DLLs, plus explicitly selected
+[raw NMOS 6502 images](raw-binary.md#nmos-6502) with a caller-supplied load address,
 on fixed local NTFS volumes. Other raw CPU families remain unsupported on Windows.
 The boundary uses bundled Job Object ownership, protected runtime DACLs, and
-handle-based path admission. See [Windows Ghidra P0](../../providers/windows-ghidra-p0.md) and
+handle-based path admission. See [Windows Ghidra P0](windows-ghidra-p0.md) and
 [issue #527](https://github.com/morluto/rea/issues/527).
 On Linux and macOS, `annotate_native_function` atomically edits a function name
 and entry comments in the ephemeral database, returning refreshed analysis
-without changing executable bytes. A Ghidra address inside a function selects
-the containing function; the name and comments are changed at its entry, not
-at the selected instruction. Annotation text must contain no NUL or
+without changing executable bytes. Annotation text must contain no NUL or
 unpaired Unicode surrogate; a rejection identifies the field and UTF-16 index
 and leaves every annotation unchanged. CRLF, supplementary Unicode characters,
 and combining characters are preserved. Windows P0 remains read-only. Ghidra has no
@@ -1288,11 +1187,6 @@ and slice commitments establish the same canonical entry. The result reports
 remain separate dimensions. Equal numeric addresses without applicable coordinate
 commitments do not establish same-entry correspondence. Inspect the retained
 source Evidence and coverage when correspondence remains ambiguous.
-When both inputs authenticate to the same Evidence ID and an applicable entry
-comparison is unavailable, the match reports `method: "same-evidence"`.
-This identifies one selected observation, not a correspondence between distinct
-records or proof of complete analysis. Unavailable facets and unestablished
-call coverage remain unknown.
 To aggregate already-retained comparison results, pass their exact IDs to
 `find_changed_behavior`, for example:

@@ -1519,8 +1413,8 @@ procedures. The CLI equivalent is
 Use `start`/`end` to constrain the inclusive address window, and continue with
 `next_cursor` until `complete` is true. Inspect `searched` for page coverage and
 skipped uninitialized blocks. A missing match does not establish absence from
-uninitialized or excluded memory. See
-[Ghidra byte search](../../providers/ghidra-provider.md#masked-byte-search) for mask and coverage
+uninitialized memory or across block boundaries. See
+[Ghidra byte search](ghidra-provider.md#masked-byte-search) for mask and coverage
 semantics. This query never executes or modifies target bytes.

 Exact-name xref lookup reports distinct candidate addresses as an input ambiguity;
@@ -82,12 +82,8 @@ override. Asset and argument decoding, padding scans, and inventory construction
 yield in bounded batches and honor caller cancellation. Asset count and name
 budgets bound retained metadata independently of stored member body sizes. The PE
 name probe reads headers from the first 64 KiB of the carrier; a PE whose
-headers extend beyond that is left to native classification. ELF note tables
-are read for at most one note per 12 carrier bytes in total, the most that
-disjoint tables can hold, so program headers that repeat the same notes do not
-rescan them once per header. Past that count the remaining tables are
-unreadable: an ELF without a confirmed blob keeps its native classification,
-and one with a blob fails closed. Snapshot and code-cache bytes remain opaque.
+headers extend beyond that is left to native classification. Snapshot and
+code-cache bytes remain opaque.

 ## Verification

@@ -1,125 +0,0 @@
-# Offline Playwright traces
-
-Use `inspect_playwright_trace` or `inspect-playwright-trace` with an existing
-local Playwright **trace v10** ZIP. Import is offline: recorded URLs are not
-requested, and no browser, application or trace viewer is started.
-
-```sh
-rea inspect-playwright-trace /absolute/trace.zip --json
-rea inspect-playwright-trace /absolute/trace.zip --detail summary \
-  --evidence_output /absolute/new-evidence.bundle.json --json
-```
-
-MCP defaults to a compact summary and retains complete supported Evidence.
-CLI defaults to complete delivery; summary and selected pages require an absent
-`--evidence_output` destination, so later queries can read the original parent.
-
-```json
-{
-  "name": "inspect_playwright_trace",
-  "arguments": {
-    "path": "/captures/trace.zip",
-    "view": {
-      "kind": "playwright-trace",
-      "collection": "events",
-      "kinds": ["network"],
-      "fields": ["method", "url", "status"],
-      "limit": 10
-    }
-  }
-}
-```
-
-`view` takes precedence over `detail`. The retained parent can be queried with
-`inspect_analysis_view`; CLI can use the same request against an exported
-Evidence bundle with `inspect-analysis-view`.
-
-## Facts, selection and text
-
-The `playwright-trace` view offers:
-
-| Collection    | Available selection                                                    |
-| ------------- | ---------------------------------------------------------------------- |
-| `events`      | Batch event/stream/call IDs, event kinds, fields, row offset and limit |
-| `streams`     | Batch stream IDs, fields and row pages                                 |
-| `members`     | Batch member IDs, exact archive paths, fields and row pages            |
-| `diagnostics` | Codes, fields and row pages                                            |
-| `event-text`  | One event ID, UTF-16 character offset and limit                        |
-
-An omitted filter selects all retained rows; an explicit empty filter selects
-none. Minimal event rows keep event/stream IDs, source member/line, producer
-ordinal, kind and credential-redaction status. Page exhaustion describes only
-the selected facts and never establishes complete recording coverage.
-
-Default event pages return at most 256 UTF-16 code units in `text_preview`,
-with explicit text coverage. Continue from that preview's `next_offset` using
-`collection: "event-text"`, its `event_id`, `offset`, and a character `limit`
-(default 2,048). Character offsets do not split surrogate pairs. Explicit
-`fields: ["text"]` returns the complete interpreted text value; `reported`
-returns the retained supported payload and sidecars remain selectable.
-Complete Evidence remains accessible through ordinary bundle operations.
-
-## Source and coverage
-
-Archive SHA-256 and directory occurrence bind stable member identity. Each event
-retains its member ID, physical one-based NDJSON line and zero-based physical
-line ordinal. Headline times retain producer monotonic milliseconds, without
-aligning stream clocks. Counts derive from the retained supported records. Call IDs are producer values; they do not establish unique actions
-across streams or imply a successfully completed before/after pair. There is no
-inferred total ordering or clock alignment between `.trace` and `.network`.
-
-Member `path` preserves the reader's original ZIP name; `logical_path` separately
-records its normalized interpretation. Resource references, exact `paths` filters
-and trace/network profile pairing use original names, so `resources/x` and
-`./resources/x` remain distinct. Reader limitations remain attached to each member
-and keep source interpretation partial when present.
-
-`decoder_profile` names the selected interpretation policy, not a verified source version.
-Trace members require an initial numeric v10 context header. Other declared
-versions are refused. Missing, malformed, repeated or ambiguous profiles remain
-unknown; network members require one unambiguous paired trace profile. Valid
-siblings of malformed records stay useful, with explicit diagnostics. Unsafe
-numeric values are not rounded: exact literals stay in sidecars.
-
-Interpreted facts cover action boundaries (class/method, title, call/page IDs,
-selected navigation URL/selector, recorded times and available error text),
-console text/location, network metadata and screencast references. Other action
-arguments, results, context options, DOM, stacks, unsupported event types and
-resource contents are outside this version's interpretation. These omissions
-are scope limitations, not assertions that omitted values are secrets or absent.
-Original archive bytes remain the complete raw source.
-
-Known HAR transport credentials and structured network, navigation and console-location
-URL userinfo are excluded using the existing capture projection. Ordinary names, query values, console text and caller data
-are preserved. Network numeric/redaction pointers are relative to `reported`;
-combine them with the event source's `record_pointer` (`/snapshot`) to locate the
-original NDJSON value. Resource-reference pointers already address the physical
-record.
-
-Resource references distinguish `present-unread`, `missing`, `ambiguous` and
-`unavailable`. Presence means directory metadata only: screenshots and bodies are
-not read or validated. Member `declared_bytes` and `declared_compressed_bytes`
-come from the ZIP directory; they are not measurements of unread payloads.
-Only decoded stream members have verified ZIP CRC and
-size. Duplicate names keep separate occurrence IDs; no filename silently picks
-a resource. Recording completeness always remains unknown, including after all
-retained pages have been read.
-
-## Bounds and verification
-
-Each decoder admits one archive import at a time; concurrent imports receive a
-retryable capacity error. Retained queries do not require another import.
-Resource policies admit a 256-MiB archive, 32 MiB of decoded streams, a
-conservative 32-MiB retained-facts representation, 4-MiB metadata reads and
-4-MiB physical lines. JSON parsing additionally checks heap headroom, a
-131,072-node record allowance and the shared 64-level capture nesting budget.
-These are resource policies, not Playwright format limits. Paging or field
-selection does not increase parsing allowances; choose a smaller complete
-recorder chunk when admission fails.
-
-The owned fixtures in `tests/fixtures/playwright-trace/` preserve actual
-Playwright 1.64.1 v10 recorder text. Public CLI/MCP tests exercise advertised
-schemas, retained and bundle queries without the source file, partial facts,
-credential exclusion, bounded Unicode previews, and a loopback listener that
-must receive no import-time requests. Recorder/version/platform compatibility
-outside this verified profile is unverified.
Author	SHA1	Message	Date
morluto	1a4db31eea	chore: combine trace and function evidence prototypes	2026-11-04 14:29:02 +08:00
morluto	2e1e99283e	fix(cli): preserve partially captured source closure	2026-11-04 14:26:17 +08:00
morluto	2e8d463400	fix(cli): retain function evidence sources in bundles	2026-11-04 14:24:09 +08:00
morluto	e62484931c	fix: bound and share source-closure checks	2026-11-04 14:17:15 +08:00
morluto	89d5bb7056	fix: revalidate restored snapshot sources lazily	2026-11-04 14:06:59 +08:00
morluto	75c7187290	fix: preserve source closure during snapshot replay	2026-11-04 13:55:45 +08:00
morluto	1fc86c45aa	docs(mcp): guide trace reference classification	2026-11-04 10:15:18 +08:00
morluto	de9d468211	docs(mcp): clarify imported residual questions	2026-11-04 10:02:56 +08:00
morluto	ec05b9de27	merge: integrate main into native trace views	2026-11-03 19:31:43 +08:00
morluto	2a0415cd5b	test(snapshot): verify linked foreign evidence stays scoped	2026-11-02 02:56:23 +08:00
morluto	673d971381	fix(snapshot): retain linked source evidence for replay	2026-11-02 02:54:41 +08:00
morluto	4809afeef5	feat(native): page retained feature traces	2026-11-02 02:43:25 +08:00