feat(native): page retained procedure references (#8588)

* feat(native): page retained feature traces

* fix(snapshot): retain linked source evidence for replay

* test(snapshot): verify linked foreign evidence stays scoped

* feat(native): page retained procedure references

* docs(mcp): clarify imported residual questions

* docs(mcp): guide trace reference classification

* fix(cli): report result sources when Evidence publication fails

A trace keeps linked sources on the result. Use those records for the
undelivered source closure as well as the bundle, so a refused output
does not report them as not captured.

* ci: rerun pull request checks

The merge of origin/main did not start the CI workflow for this head.

* fix(native): document shared procedure endpoints and the required selector

Describe kind shared and items.endpoints instead of inline procedure copies.
State that procedure-references requires a positional selector or --procedure.

* fix(native): count procedure-reference endpoints before keeping a row

Include the shared endpoint table in the page budget, with JSON punctuation,
and store a new procedure only when its row is accepted.

* fix(native): measure a procedure endpoint once before its comparison key

Size the candidate before building one canonical identity, and reuse that
key for the selected-procedure and shared-endpoint checks.

* fix(native): reject an oversized procedure endpoint before canonicalizing it

When the JSON size already exceeds every stored identity, skip the canonical
string and keep the row out of the page.

* fix(native): describe procedure-reference direction and coverage

Avoid execution wording in the tool description, and give the CLI direction
option the help text the catalog requires.

* fix(native): compare endpoint size with UTF-8 identity length

Keep one running maximum of stored identity bytes. A multibyte selected
procedure is recognized when its JSON no longer fits the page.

* test(cli): count procedure-references as a dedicated command

The MCP tool has a CLI command, so it is no longer an MCP-only exception.

* test(native): catch the string-length endpoint comparison

Use a 200,000-character multibyte selected procedure and a shorter ASCII
endpoint so the old JavaScript length check drops the selected row.

* ci: rerun after the binary-layout toolchain timeout

The required check failed because the toolchain install exceeded 15 minutes.
The same job completed on the previous head, and this commit does not change
the procedure-reference behavior.

* test: stabilize capture decoder exhaustion coverage

---------

Co-authored-by: Cursor Agent <[email protected]>

.agents/skills/rea-analysis-optimization/SKILL.md

@@ -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/tool-design.md), and
-[testing guide](../../../docs/testing.md). This skill supplies an optimization
+[tool design](../../../docs/development/tool-design.md), and
+[testing guide](../../../docs/development/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.
 

.agents/skills/rea-changelog-update/SKILL.md

@@ -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/releasing.md](../../../docs/releasing.md) from the repository root for
+[docs/development/releasing.md](../../../docs/development/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.
 

.agents/skills/rea-ci-tests-audit/SKILL.md

@@ -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/testing.md),
+Follow the checkout's `AGENTS.md`, [testing guide](../../../docs/development/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;

.agents/skills/rea-tool-design/SKILL.md

@@ -5,7 +5,7 @@ description: Audit, investigate, design, or change REA investigation tools, CLI/
 
 # REA tool design
 
-Use the [tool-design guide](../../../docs/tool-design.md) for tool boundaries,
+Use the [tool-design guide](../../../docs/development/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.
@@ -14,12 +14,12 @@ 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/tool-design.md#design-recovery-around-the-failure).
-Use [workflow verification](../../../docs/testing.md#provider-backed-workflow-verification)
+failure](../../../docs/development/tool-design.md#design-recovery-around-the-failure).
+Use [workflow verification](../../../docs/development/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/tool-design.md#audit-existing-tools):
+For an audit, follow [audit existing tools](../../../docs/development/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
@@ -30,7 +30,7 @@ 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/testing.md)
+For implementation or verification, consult [testing](../../../docs/development/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.

.agents/skills/reverse-engineer-anything/SKILL.md

@@ -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/firmware-analysis.md).
+  Linux; see the [firmware guide](https://github.com/morluto/rea/blob/main/docs/guides/firmware/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;
@@ -150,7 +150,7 @@ 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/web-network-captures.md) for the exact upstream
+  [historical captures](https://github.com/morluto/rea/blob/main/docs/guides/web/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 +165,7 @@ 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/packet-captures.md).
+  [capture guide](https://github.com/morluto/rea/blob/main/docs/guides/data/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 +173,7 @@ 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/pcap-analysis.md).
+  [packet summaries](https://github.com/morluto/rea/blob/main/docs/guides/data/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 +181,7 @@ 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/signal-recordings.md).
+  `REA_SIGROK_COMMAND`; see [recording guide](https://github.com/morluto/rea/blob/main/docs/guides/signals/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 +190,7 @@ 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/wasm-artifacts.md).
+  See the [WASM guide](https://github.com/morluto/rea/blob/main/docs/guides/wasm/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 +209,13 @@ 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/evm-bytecode.md).
+  [EVM bytecode guide](https://github.com/morluto/rea/blob/main/docs/guides/evm/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/go-binaries.md).
+  [Go binary guide](https://github.com/morluto/rea/blob/main/docs/guides/native/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`
@@ -332,17 +332,17 @@ 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/sqlite-databases.md).
+  [SQLite guide](https://github.com/morluto/rea/blob/main/docs/guides/data/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/binary-diagnostics.md).
+  [offline binary guide](https://github.com/morluto/rea/blob/main/docs/guides/native/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/recorded-crashes.md).
+  [recorded crash guide](https://github.com/morluto/rea/blob/main/docs/guides/native/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 +358,9 @@ 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/ida-provider.md).
+[IDA provider guide](https://github.com/morluto/rea/blob/main/docs/providers/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/ida-provider.md#migrate-a-legacy-attached-registration).
+[legacy attached migration](https://github.com/morluto/rea/blob/main/docs/providers/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.

.agents/skills/reverse-engineer-anything/references/android-applications.md

@@ -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/android-analysis.md#link-native-declarations-to-jni-candidates).
+[JNI guide](https://github.com/morluto/rea/blob/main/docs/guides/android/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

.agents/skills/reverse-engineer-anything/references/connection-and-recovery.md

@@ -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/client-configuration.md#client-tool-names-and-discovery).
+[client tool names and discovery](https://github.com/morluto/rea/blob/main/docs/getting-started/client-configuration.md#client-tool-names-and-discovery).
 
 ## Choose the remedy from the observed failure
 

.agents/skills/reverse-engineer-anything/references/evidence-workflows.md

@@ -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/cli.md#import-export-and-compare-evidence).
+[CLI reuse guide](https://github.com/morluto/rea/blob/main/docs/getting-started/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"]}`.

.agents/skills/reverse-engineer-anything/references/javascript-applications.md

@@ -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/javascript-recovery.md).
+caller-supplied Wakaru on Linux x64; see [the recovery guide](https://github.com/morluto/rea/blob/main/docs/guides/javascript/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

.agents/skills/reverse-engineer-anything/references/native-and-artifacts.md

@@ -246,7 +246,7 @@ 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/sqlite-databases.md).
+before inspection. See [SQLite snapshots](https://github.com/morluto/rea/blob/main/docs/guides/data/sqlite-databases.md).
 
 ## Recorded Linux crashes
 
@@ -261,7 +261,7 @@ 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/recorded-crashes.md)
+[recorded crashes](https://github.com/morluto/rea/blob/main/docs/guides/native/recorded-crashes.md)
 for exact upstream profiles, bounds and verification coverage.
 
 ## Offline ELF layout
@@ -325,7 +325,8 @@ 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
+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
@@ -393,7 +394,7 @@ 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/installation.md#automatically-checkpoint-an-owned-ghidra-program).
+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
@@ -414,7 +415,7 @@ 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/installation.md#reuse-an-existing-ghidra-project).
+[setup and preparation guide](https://github.com/morluto/rea/blob/main/docs/getting-started/installation.md#reuse-an-existing-ghidra-project).
 
 ## Ghidra startup deadline recovery
 
@@ -448,7 +449,7 @@ 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/mcp-contracts.md#ghidra-first-query-deadlines-and-recovery).
+[deadline and client guide](https://github.com/morluto/rea/blob/main/docs/reference/mcp-contracts.md#ghidra-first-query-deadlines-and-recovery).
 
 ## Bridge request ceiling
 
@@ -599,7 +600,7 @@ 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/ghidra-nativeaot.md)
+[NativeAOT guide](https://github.com/morluto/rea/blob/main/docs/providers/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
@@ -628,7 +629,7 @@ 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/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/reference/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
@@ -656,7 +657,7 @@ 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/ghidra-dos.md).
+context. PSP/stack/device state remains unmodeled. See [DOS guide](https://github.com/morluto/rea/blob/main/docs/providers/ghidra-dos.md).
 
 Use `inspect_byte_entropy` to triage high- and low-entropy ranges before extraction.
 
@@ -670,7 +671,7 @@ 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/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/providers/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
@@ -684,6 +685,11 @@ numbering gaps leave coverage unknown; a DfuSe suffix CRC mismatch follows
 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.
+
 For `compare_functions`, obtain `analyze_function` Evidence before and after the
 edit while the MCP session is open; annotation Evidence is not a comparison
 input. Export the needed Evidence before close if comparison will happen later.
@@ -704,7 +710,7 @@ 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/binary-diagnostics.md).
+[offline binary diagnostics](https://github.com/morluto/rea/blob/main/docs/guides/native/binary-diagnostics.md).
 
 ## Offline PE and ELF export tables
 
@@ -714,7 +720,7 @@ 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/binary-diagnostics.md).
+[offline binary diagnostics](https://github.com/morluto/rea/blob/main/docs/guides/native/binary-diagnostics.md).
 
 For exact core-module import/export differences, use `compare_wasm_interfaces`
 with two complete inspection Evidence records (or current-session retained

.agents/skills/reverse-engineer-anything/references/runtime-observation.md

@@ -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/frida-instrumentation.md),
+Detailed contracts and prerequisites: [Frida](https://github.com/morluto/rea/blob/main/docs/guides/runtime/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/process-capture.md),
-and [native calls/UI](https://github.com/morluto/rea/blob/main/docs/native-investigation.md#native-desktop-observation).
+[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).
 
 ## 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/web-network-captures.md)
+recorded run. See the [capture and MCP guide](https://github.com/morluto/rea/blob/main/docs/guides/web/web-network-captures.md)
 for the workflow and Telerik's public setup and traffic-debugging skills.

.github/ISSUE_TEMPLATE/documentation.yml

@@ -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/mcp-contracts.md
+      placeholder: README.md#quick-start or docs/reference/mcp-contracts.md
     validations:
       required: true
 

.github/pull_request_template.md

@@ -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/testing.md#boundary-regressions)
-and [lifecycle regressions](https://github.com/morluto/rea/blob/main/docs/testing.md#lifecycle-regressions)
+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)
 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/releasing.md. -->
+  See docs/development/releasing.md. -->
 - Real Hopper/Ghidra, browser, or OS coverage:
 - Package or release metadata impact:
 - Security, privacy, process, or containment review:

.github/workflows/ci.yml

@@ -1016,8 +1016,8 @@ jobs:
         uses: ./.github/actions/npm-cache
       - run: npm ci
       - run: npm run docs:check
-      - name: Render documentation and validate page links
-        run: npm run docs:build
+      - name: Verify published routes, source links and local anchors
+        run: npm run verify:docs:routes
       - name: Generation leaves authored files unchanged
         run: git diff --exit-code
       - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2

.github/workflows/pages.yml

@@ -27,4 +27,4 @@ jobs:
         id: npm-cache
         uses: ./.github/actions/npm-cache
       - run: npm ci
-      - run: npm run docs:build
+      - run: npm run verify:docs:routes

AGENTS.md

@@ -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.mermaid](docs/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/architecture.mermaid](docs/architecture/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/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.
+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.
 
 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.
 
@@ -68,6 +68,12 @@ 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.
@@ -80,15 +86,15 @@ 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/testing.md#checking-installers-and-publisher-downloads).
+[Checking installers and publisher downloads](docs/development/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/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/development/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/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 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 user- or agent-facing tool problems, prioritize fixing the owning behavior,
 contract, and actionable result or recovery at the point of use. Document the
@@ -96,7 +102,7 @@ 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/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.
+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.
 
 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.
 

CHANGELOG.md

@@ -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/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.
+- **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.
 - **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/testing.md).
+Provider prerequisites and recorded verification scope are listed in [the testing guide](docs/development/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/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/providers/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/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/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.
 
 - **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/process-capture.md) and [browser scenario contract](docs/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/guides/runtime/process-capture.md) and [browser scenario contract](docs/guides/web/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/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/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.
 
 * **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))

CONTRIBUTING.md

@@ -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.mermaid). It is not a complete directory or
+[architecture map](docs/architecture/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/tool-design.md#interpret-boundary-facts-once)
+See [interpreting boundary facts once](docs/development/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/tool-design.md) and preserve the canonical contracts and generated catalog.
+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 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/installation.md#start-setup).
+[installation](docs/getting-started/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.
 
@@ -289,16 +289,20 @@ 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/testing.md#developer-commands) for command scopes
+[testing](docs/development/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/firmware-analysis.md#windows-submodule-checkout),
+[Unblob checkout workaround](docs/guides/firmware/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/`.
@@ -352,7 +356,7 @@ 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/testing.md#developer-commands)
+select relevant boundary tests explicitly. See [testing](docs/development/testing.md#developer-commands)
 for commands, test placement, pruning, and real-provider prerequisites.
 
 Before requesting review, run relevant tests and `npm run check`; add
@@ -427,8 +431,8 @@ 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/testing.md#end-to-end-integration-and-golden-evidence)
-for prerequisites and scope, and [Hopper setup](docs/installation.md#hopper)
+[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)
 for supported hosts and unattended startup.
 
 Use the default `build/conformance/manifest.json` unless explicitly verifying
@@ -437,7 +441,7 @@ Generated fixtures and manifests remain ignored.
 
 ## Maintainer release checklist
 
-Use the [release guide](docs/releasing.md). Main pushes automatically refresh a
+Use the [release guide](docs/development/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.
 

README.md

@@ -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/mcp-contracts.md#generated-catalog)
+[![MCP tool catalog](https://img.shields.io/badge/MCP-tool_catalog-5c4ee5?style=flat-square)](docs/reference/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/installation.md` under
+checks. Recovery steps are in `docs/getting-started/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/installation.md#supported-agents). See
-[installation and setup](docs/installation.md) for provider configuration and
+[other agents](docs/getting-started/installation.md#supported-agents). See
+[installation and setup](docs/getting-started/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/cli.md) for native commands, provider selection,
+[CLI and Evidence guide](docs/getting-started/cli.md) for native commands, provider selection,
 snapshots and scripting.
 
 ### Update REA
@@ -191,45 +191,45 @@ 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/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)                                                                        |
-| 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/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)                                              |
+| 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)                                                                             |
 
 Static JavaScript and .NET inspection read the supplied files without running
 the application. Runtime capture runs or interacts with the selected target
@@ -243,15 +243,15 @@ 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/installation.md#hopper), the
-[IDA guide](docs/ida-provider.md) (including an optional native MCP bridge), the
+[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
 [Kuna decompiler guide](docs/kuna-provider.md), and
-[experimental Windows Ghidra support](docs/windows-ghidra-p0.md).
-Ghidra also supports [16-bit DOS analysis](docs/ghidra-dos.md).
+[experimental Windows Ghidra support](docs/providers/windows-ghidra-p0.md).
+Ghidra also supports [16-bit DOS analysis](docs/providers/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/cli.md#choose-a-provider).
-Check [release availability](docs/installation.md#released-package-and-main)
+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 features added since the latest npm release.
 
 ## Showcases
@@ -341,8 +341,8 @@ 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/installation.md#supported-agents); other clients can use
-[manual MCP registration](docs/installation.md#mcp-registry).
+[supported agents](docs/getting-started/installation.md#supported-agents); other clients can use
+[manual MCP registration](docs/getting-started/installation.md#mcp-registry).
 
 </details>
 
@@ -352,7 +352,7 @@ 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/installation.md#hopper)
+use your existing installations. See [provider setup](docs/getting-started/installation.md#hopper)
 for the options and their supported targets.
 
 </details>
@@ -364,7 +364,7 @@ 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/installation.md#launcher-paths-and-troubleshooting).
+[Hopper startup and troubleshooting](docs/getting-started/installation.md#launcher-paths-and-troubleshooting).
 
 </details>
 
@@ -373,7 +373,7 @@ 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/installation.md#skill-only-installation).
+your agent. See [skill-only installation](docs/getting-started/installation.md#skill-only-installation).
 
 </details>
 
@@ -422,12 +422,12 @@ 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/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.
+- [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.
 
 Report vulnerabilities through [SECURITY.md](SECURITY.md).
 
@@ -462,8 +462,8 @@ 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/testing.md) for verification lanes, and the
-[architecture map](docs/architecture.mermaid) for selected layers and dependency paths.
+[testing](docs/development/testing.md) for verification lanes, and the
+[architecture map](docs/architecture/architecture.mermaid) for selected layers and dependency paths.
 
 ## License
 

SECURITY.md

@@ -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/windows-ghidra-p0.md#private-runtime-transport-and-lifecycle).
+the current user and SYSTEM. See [Windows Ghidra P0](docs/providers/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

THIRD_PARTY_NOTICES.md

@@ -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/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/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.                                                                                                                                                                                                                 |
 
 Ghidra's original notice credits software developed at the National Security
 Agency. It explains that US-government-created portions are not subject to US

bridge/ghidra/ReaGhidraBridge.java

@@ -179,6 +179,7 @@ public final class ReaGhidraBridge extends HeadlessScript {
     private List<FunctionEntry> procedureInventory;
     private List<InventoryItem> stringInventory;
     private DecompInterface decompiler;
+    private boolean existingProject;
     // 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. */
@@ -199,6 +200,7 @@ public final class ReaGhidraBridge extends HeadlessScript {
         Path descriptorPath = Path.of(arguments[0]);
         checkpointDirectory = descriptorPath.toAbsolutePath().normalize().getParent();
         SessionDescriptor descriptor = readDescriptor(descriptorPath);
+        existingProject = descriptor.existingProject;
         decompileTimeoutSeconds = descriptor.decompileTimeoutSeconds();
         // Windows retains a native immutable bearer descriptor lease until
         // runtime_close; POSIX removes it after this read. Normal cleanup removes
@@ -876,6 +878,7 @@ public final class ReaGhidraBridge extends HeadlessScript {
         JsonArray blocks = new JsonArray();
         JsonArray skipped = new JsonArray();
         JsonArray notLoaded = new JsonArray();
+        JsonArray overlays = new JsonArray();
         List<ByteSearchBlock> eligible = new ArrayList<>();
         for (MemoryBlock block : ordered) {
             monitor.checkCancelled();
@@ -883,10 +886,16 @@ public final class ReaGhidraBridge extends HeadlessScript {
             Address high = block.getEnd();
             Address bound = start == null ? end : start;
             if (bound != null && !bound.getAddressSpace().equals(low.getAddressSpace())) continue;
-            if (bound == null && (!block.isLoaded() || block.isOverlay())) {
+            // Without bounds, search loaded non-overlay memory. Unloaded file
+            // parts and loaded overlays stay reachable through explicit bounds.
+            if (bound == null && !block.isLoaded()) {
                 notLoaded.add(byteSearchCoverage(block, low, high));
                 continue;
             }
+            if (bound == null && block.isOverlay()) {
+                overlays.add(byteSearchCoverage(block, low, high));
+                continue;
+            }
             if (start != null && low.compareTo(start) < 0) low = start;
             if (end != null && high.compareTo(end) > 0) high = end;
             if (low.compareTo(high) > 0) continue;
@@ -960,6 +969,7 @@ public final class ReaGhidraBridge extends HeadlessScript {
         searched.addProperty("bytes", covered);
         searched.add("skipped_uninitialized", skipped);
         searched.add("skipped_not_loaded", notLoaded);
+        searched.add("skipped_overlays", overlays);
         JsonObject result = new JsonObject();
         result.add("matches", matches);
         result.add("searched", searched);
@@ -1414,8 +1424,29 @@ public final class ReaGhidraBridge extends HeadlessScript {
         flow.addProperty("conditional", false);
         flow.addProperty("computed", false);
         if (instruction == null) {
-            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");
+            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);
+            }
             for (String key : List.of("bytes", "length", "mnemonic", "raw_disassembly")) result.add(key, JsonNull.INSTANCE);
         } else {
             result.addProperty("status", "decoded");
@@ -2376,7 +2407,7 @@ public final class ReaGhidraBridge extends HeadlessScript {
                 if (!match.matched()) {
                     continue;
                 }
-                JsonObject item = resultItem(entry.item, null);
+                JsonObject item = resultItem(entry.item, "procedure");
                 if (!match.aliases().isEmpty()) {
                     JsonArray aliases = new JsonArray();
                     for (String alias : match.aliases()) aliases.add(alias);
@@ -2391,7 +2422,7 @@ public final class ReaGhidraBridge extends HeadlessScript {
             if (!matcher.matches(item.value)) {
                 continue;
             }
-            items.add(resultItem(item, null));
+            items.add(resultItem(item, procedureSearch ? "procedure" : "string"));
         }
         return items;
     }
@@ -3716,7 +3747,7 @@ public final class ReaGhidraBridge extends HeadlessScript {
         return result;
     }
 
-    private static JsonObject callRelationshipCoverage(
+    private JsonObject callRelationshipCoverage(
             CallBoundaryObservation calls, Integer missingCallers) {
         JsonObject coverage = completeResolvedCallCoverage();
         Integer omitted = calls == null ? null : calls.unrepresentedCalleeCalls();
@@ -3733,7 +3764,7 @@ public final class ReaGhidraBridge extends HeadlessScript {
             if (calls == null && missingCallers == null) directions.add("callers");
             directions.add("callees");
             coverage.add("limited_directions", directions);
-            return coverage;
+            return qualifyProjectCallCoverage(coverage, calls, missingCallers);
         }
         JsonArray limitations = new JsonArray();
         if (callerLimitation != null) limitations.add(callerLimitation);
@@ -3747,6 +3778,35 @@ public final class ReaGhidraBridge extends HeadlessScript {
             coverage.add("limitations", limitations);
             coverage.add("limited_directions", directions);
         }
+        return qualifyProjectCallCoverage(coverage, calls, missingCallers);
+    }
+
+    private JsonObject qualifyProjectCallCoverage(
+            JsonObject coverage, CallBoundaryObservation calls, Integer missingCallers) {
+        if (!existingProject) return coverage;
+        String reason = "The selected project's prior analysis completeness is unknown; " +
+            "the recorded call relationships may omit undiscovered callers or callees.";
+        String status = coverage.get("status").getAsString();
+        // A single-direction read with known omissions is still partial; an
+        // unknown project history adds a limitation rather than erasing them.
+        if (status.equals("partial") && (calls == null || missingCallers == null)) {
+            coverage.getAsJsonArray("limitations").add(reason);
+            return coverage;
+        }
+        if (status.equals("unknown")) reason += " " + coverage.get("reason").getAsString();
+        if (status.equals("partial")) {
+            for (JsonElement limitation : coverage.getAsJsonArray("limitations"))
+                reason += " " + limitation.getAsString();
+        }
+        JsonArray directions = new JsonArray();
+        if (missingCallers != null || (calls == null && missingCallers == null))
+            directions.add("callers");
+        if (calls != null || (calls == null && missingCallers == null))
+            directions.add("callees");
+        coverage.addProperty("status", "unknown");
+        coverage.addProperty("reason", reason);
+        coverage.remove("limitations");
+        coverage.add("limited_directions", directions);
         return coverage;
     }
 

bridge/ghidra/ReaGhidraRiscvCallingConvention.java

@@ -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/ghidra-riscv.md state. The
+ * program's own default prototype, as its {@link Policy} row and docs/providers/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.
  */

bridge/native/rea_lldb_tracer.py

@@ -243,6 +243,20 @@ 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()
@@ -256,6 +270,7 @@ 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
 

bridge/native/test_rea_lldb_tracer.py

@@ -25,6 +25,45 @@ 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):
@@ -390,6 +429,9 @@ class NativeTraceBudgetTests(unittest.TestCase):
                 return FileSpec()
 
         class Address:
+            def GetLineEntry(self):
+                return types.SimpleNamespace(IsValid=lambda: False)
+
             def GetModule(self):
                 return Module()
 
@@ -491,7 +533,24 @@ 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()
 
@@ -518,19 +577,35 @@ class NativeTraceBudgetTests(unittest.TestCase):
         breakpoint_count = 1000
         created = [[Breakpoint()] for _ in range(breakpoint_count)]
         config = {"breakpoints": [{"kind": "objc-method"}] * breakpoint_count}
-        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)
+        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"]
+                        )
+                    )
 
 
 if __name__ == "__main__":

bridge/pwndbg/test_core_context.py

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

docs/.vitepress/config.ts

@@ -1,4 +1,18 @@
 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",
@@ -6,135 +20,92 @@ 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: "Getting started",
+        text: "Documentation directory",
         items: [
-          { 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: "Binary hardening", link: "/binary-hardening" },
-          { 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: "Desktop application capture",
-            link: "/desktop-application-capture",
-          },
-          {
-            text: "Desktop application state",
-            link: "/desktop-application-state",
-          },
-          {
-            text: "Desktop application export",
-            link: "/desktop-application-export",
-          },
-          {
-            text: "Desktop application tasks",
-            link: "/desktop-application-tasks",
-          },
-          {
-            text: "Desktop build computer",
-            link: "/desktop-build-computer",
-          },
-          {
-            text: "Building and witnessing",
-            link: "/desktop-build-witness",
-          },
-          { 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" },
+          { text: "All guides", link: "/documentation" },
+          { text: "Authoring conventions", link: "/development/documentation" },
+          { text: "Feature specifications", link: "/specs/" },
+          { text: "Architecture decisions", link: "/adr/" },
         ],
       },
+      ...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: [

docs/.vitepress/documentation.ts

@@ -0,0 +1,654 @@
+// 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]];
+    }),
+  ),
+);

docs/README.md

@@ -0,0 +1,195 @@
+# 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)

docs/adr/README.md

@@ -0,0 +1,9 @@
+# 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.

docs/agent-environments-quickstart.md

@@ -11,14 +11,14 @@ with your RL framework to set task goals, check rewards, and run training.
 
 ## Before you start
 
-Install [REA and its agent integration](installation.md). To record an app,
+Install [REA and its agent integration](getting-started/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](testing.md#exported-environment-bundles)
+and start Docker. REA's [compatibility check](development/testing.md#exported-environment-bundles)
 uses AgentEnv version `0.9.1431` with Python 3.12.
 
 There are two ways to build an environment: ask your agent to record the app,
@@ -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](#3-run-the-environment). The next section is an
+[run the environment](#run-the-environment). The next section is an
 alternative for an existing recording.
 
 ## 2. Or build from a saved recording
@@ -91,6 +91,8 @@ 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

docs/agent-environments.md

@@ -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](web-network-captures.md#environment-manifest) view from
+[environment manifest](guides/web/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](web-network-captures.md#environment-coverage) view
+[environment coverage](guides/web/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](browser-scenario-contract.md) records a scripted session
+[browser scenario](guides/web/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](browser-scenario-contract.md#request-steps): each
+calls with [request steps](guides/web/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](web-network-captures.md#environment-state) view extracts
+[environment state](guides/web/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`](cli.md#serve-mcp-over-streamable-http) resolves them. The
+[`rea mcp --http`](getting-started/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](mcp-contracts.md#transports) describes.
+and shutdown contract as [transports](reference/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](web-network-captures.md#environment-state)'s list rule (the
+[environment state](guides/web/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](web-network-captures.md#environment-state) the capture
+[environment state](guides/web/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](web-network-captures.md#environment-state) for them is served:
+[write plan](guides/web/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
@@ -1187,7 +1187,7 @@ 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](testing.md#exported-environment-bundles). It projects
+described in [testing](development/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

docs/apple-ips.md

@@ -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](recorded-crashes.md) workflow.
+use the separate [recorded crash](guides/native/recorded-crashes.md) workflow.
 
 ## Limits and failures
 

docs/ci-analysis.md

@@ -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](cli.md#output-and-exit-status).
+coverage before making such a decision. See [output and exit status](getting-started/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](installation.md); do not silently switch providers,
+[documented prerequisites](getting-started/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

docs/design/limits-and-recovery.md

@@ -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](../mcp-contracts.md#editable-analysis-settings); recorded runtime
+[MCP contracts](../reference/mcp-contracts.md#editable-analysis-settings); recorded runtime
 checks and their limitations are in the
 [verification report](../verification/runtime-analysis-settings.md).
 
@@ -399,7 +399,7 @@ 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](../testing.md#test-design-and-pruning) for the assertion policy.
+See [test design](../development/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

docs/desktop-application-export.md

@@ -310,8 +310,8 @@ 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 nested more than 500 levels deep, gets an `error` instead of a view, as in
-REA, while text that is not one JSON
+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

docs/development/client-verification.md

@@ -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](client-configuration.md#launchers-and-path).
+separately from terminal doctor results. See [launcher troubleshooting](../getting-started/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](mcp-contracts.md#compact-input-schema-profile)
+choice is preserved. See the [compact input schema profile](../reference/mcp-contracts.md#compact-input-schema-profile)
 for details of its reduced forms.
 
 Custom renderer hosts can raise `inputMaxChars` through `renderToolSignature` or
@@ -47,7 +47,7 @@ and [renderer usage notes](https://github.com/earendil-works/pi/blob/b45e0ebcc5a
 
 ## llama.cpp
 
-The [manual stdio connection](client-configuration.md#llamacpp) was checked on
+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
@@ -486,7 +486,7 @@ 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](website-script-export.md).
+both public adapters. See [website script export](../guides/web/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 +494,7 @@ 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](website-module-trace.md).
+Chrome CI include this verifier. See [module relationships](../guides/web/website-module-trace.md).
 
 ## Agent evaluation and conformance records
 

docs/development/documentation.md

@@ -0,0 +1,82 @@
+# 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.

docs/development/releasing.md

@@ -192,7 +192,7 @@ registry metadata or changelog disagrees with that version before creating a tag
 
 Before publishing a candidate, review its changelog's breaking changes and the
 migration notes for the release being prepared. The
-[6.1 to 6.2 migration guide](migration-6.2.md) records that release's changes;
+[6.1 to 6.2 migration guide](../migrations/migration-6.2.md) records that release's changes;
 it is a historical reference, not the compatibility checklist for later releases.
 
 REA uses Release Please's `always-bump-minor` strategy: every release increments

docs/development/roadmap.md

@@ -5,8 +5,8 @@ The [platform tracker](https://github.com/morluto/rea/issues/32),
 [browser tracker](https://github.com/morluto/rea/issues/39) track capability and
 verification work. Available tools and setup are documented in the
 [investigation guides](https://rea.tools/guides/),
-[installation guide](installation.md), and
-[generated catalog](mcp-contracts.md#generated-catalog).
+[installation guide](../getting-started/installation.md), and
+[generated catalog](../reference/mcp-contracts.md#generated-catalog).
 
 ## Priorities
 
@@ -27,7 +27,7 @@ fixture servers; custom orchestration needs a demonstrated requirement.
 Provider and platform claims require their corresponding
 [real verification lanes](testing.md#real-toolchain-verification-lanes).
 See [tool design](tool-design.md) for choosing a tool boundary and
-[Ghidra semantics](ghidra-provider.md) for the existing deep-provider contract.
+[Ghidra semantics](../providers/ghidra-provider.md) for the existing deep-provider contract.
 
 Setup remains additive, reuses existing tools, and requires approval for disclosed
 configuration and Hopper installation changes. Additional installer choices need

docs/development/testing.md

@@ -8,7 +8,7 @@ installed-client and agent runs.
 Historical verification records may refer to `experiments/analysis-efficiency`.
 Those experiment scripts are available in the [archived source tree](https://github.com/morluto/rea/tree/a2e2c29b59e8775b0e6aedb09a9eb16adf32646b/experiments/analysis-efficiency);
 they are not included in current checkouts. The retained [test support](https://github.com/morluto/rea/blob/main/tests/support/analysis-efficiency/README.md)
-contains deterministic checkers and fixtures. The [allocation report](verification/analysis-efficiency/mcp-integer-allocation.md)
+contains deterministic checkers and fixtures. The [allocation report](../verification/analysis-efficiency/mcp-integer-allocation.md)
 and its original receipt JSON remain documentation, checked by the report producer.
 
 ## Developer commands
@@ -382,7 +382,7 @@ instrumentation remains equivalent.
 
 ## CodeQL production scope
 
-[The production configuration](../.github/codeql/production.yml) excludes
+[The production configuration](https://github.com/morluto/rea/blob/main/.github/codeql/production.yml) excludes
 `tests/`, `scripts/fixtures/`, `*.test.*`, `*.fixture.*`, `test_*.py`, and `*_test.py` inputs
 during extraction. It retains the default queries and the existing `local`
 threat model. Production source, bridges, runtime scripts, installation and
@@ -398,7 +398,7 @@ These exclusions do not change which behavioral tests CI executes. CodeQL's
 JavaScript/TypeScript, Python, and Actions lanes do not add shell, Java, or Swift
 analysis; their existing checks remain responsible for those languages.
 
-[The production workflow](../.github/workflows/codeql.yml) is inactive until a
+[The production workflow](https://github.com/morluto/rea/blob/main/.github/workflows/codeql.yml) is inactive until a
 repository administrator disables CodeQL **default setup** and sets the Actions
 repository variable `REA_CODEQL_ADVANCED` to `true`. Disable default setup first:
 it rejects advanced CodeQL uploads. Then enable the variable and manually run
@@ -909,7 +909,7 @@ covers deterministic evaluator logic.
 reconstruction, native-boundary relationships and application graphs without
 executing fixture PE files. Operator-local manifests and actual ILSpy oracles
 remain optional, separately reported checks; the real Ghidra NativeAOT lane has
-its own toolchain prerequisites. See [the managed guide](managed-code-analysis.md)
+its own toolchain prerequisites. See [the managed guide](../guides/managed/managed-code-analysis.md)
 for those configurations. Generated completion-ledger checks use the same owning
 entrypoint and include its verifier/fixture files in their cache inputs.
 
@@ -1165,104 +1165,104 @@ public registry, and checks both the primary failure and live descendant absence
 
 ## Real-toolchain verification lanes
 
-See [Real-toolchain verification lanes](testing-lanes.md#real-toolchain-verification-lanes).
+See [Real-toolchain verification lanes](../testing-lanes.md#real-toolchain-verification-lanes).
 
 ## Android APK analysis
 
-See [Android APK analysis](testing-lanes.md#android-apk-analysis).
+See [Android APK analysis](../testing-lanes.md#android-apk-analysis).
 
 ## Apktool resource decoding
 
-See [Apktool resource decoding](testing-lanes.md#apktool-resource-decoding).
+See [Apktool resource decoding](../testing-lanes.md#apktool-resource-decoding).
 
 ## Flutter build identification
 
-See [Flutter build identification](testing-lanes.md#flutter-build-identification).
+See [Flutter build identification](../testing-lanes.md#flutter-build-identification).
 
 ## ADB device acquisition
 
-See [ADB device acquisition](testing-lanes.md#adb-device-acquisition).
+See [ADB device acquisition](../testing-lanes.md#adb-device-acquisition).
 
 ## Optional NativeAOT Ghidra analysis
 
-See [Optional NativeAOT Ghidra analysis](testing-lanes.md#optional-nativeaot-ghidra-analysis).
+See [Optional NativeAOT Ghidra analysis](../testing-lanes.md#optional-nativeaot-ghidra-analysis).
 
 ## IDA MCP adapter
 
-See [IDA MCP adapter](testing-lanes.md#ida-mcp-adapter).
+See [IDA MCP adapter](../testing-lanes.md#ida-mcp-adapter).
 
 ## Kuna lane
 
-See [Kuna lane](testing-lanes.md#kuna-lane).
+See [Kuna lane](../testing-lanes.md#kuna-lane).
 
 ## DOS Ghidra analysis
 
-See [DOS Ghidra analysis](testing-lanes.md#dos-ghidra-analysis).
+See [DOS Ghidra analysis](../testing-lanes.md#dos-ghidra-analysis).
 
 ## Apple Interface Builder archives
 
-See [Apple Interface Builder archives](testing-lanes.md#apple-interface-builder-archives).
+See [Apple Interface Builder archives](../testing-lanes.md#apple-interface-builder-archives).
 
 ## Native platform baseline in CI
 
-See [Native platform baseline in CI](testing-lanes.md#native-platform-baseline-in-ci).
+See [Native platform baseline in CI](../testing-lanes.md#native-platform-baseline-in-ci).
 
 ### Termux Android browser smoke test
 
-See [Termux Android browser smoke test](testing-lanes.md#termux-android-browser-smoke-test).
+See [Termux Android browser smoke test](../testing-lanes.md#termux-android-browser-smoke-test).
 
 ## Packet capture analysis
 
-See [Packet capture analysis](testing-lanes.md#packet-capture-analysis).
+See [Packet capture analysis](../testing-lanes.md#packet-capture-analysis).
 
 ## Apple native metadata and UI
 
-See [Apple native metadata and UI](testing-lanes.md#apple-native-metadata-and-ui).
+See [Apple native metadata and UI](../testing-lanes.md#apple-native-metadata-and-ui).
 
 ### Firmware adapters
 
-See [Firmware adapters](testing-lanes.md#firmware-adapters).
+See [Firmware adapters](../testing-lanes.md#firmware-adapters).
 
 ### JavaScript source recovery
 
-See [JavaScript source recovery](testing-lanes.md#javascript-source-recovery).
+See [JavaScript source recovery](../testing-lanes.md#javascript-source-recovery).
 
 ### Captured website source-map lane
 
-See [Captured website source-map lane](testing-lanes.md#captured-website-source-map-lane).
+See [Captured website source-map lane](../testing-lanes.md#captured-website-source-map-lane).
 
 ### JavaScript large-output lane
 
-See [JavaScript large-output lane](testing-lanes.md#javascript-large-output-lane).
+See [JavaScript large-output lane](../testing-lanes.md#javascript-large-output-lane).
 
 ### Website runtime attribution lane
 
-See [Website runtime attribution lane](testing-lanes.md#website-runtime-attribution-lane).
+See [Website runtime attribution lane](../testing-lanes.md#website-runtime-attribution-lane).
 
 ### Offline binary layout
 
-See [Offline binary layout](testing-lanes.md#offline-binary-layout).
+See [Offline binary layout](../testing-lanes.md#offline-binary-layout).
 
 ### Offline EVM interface
 
-See [Offline EVM interface](testing-lanes.md#offline-evm-interface).
+See [Offline EVM interface](../testing-lanes.md#offline-evm-interface).
 
 ### Recorded crash evidence
 
-See [Recorded crash evidence](testing-lanes.md#recorded-crash-evidence).
+See [Recorded crash evidence](../testing-lanes.md#recorded-crash-evidence).
 
 ### Exported environment bundles
 
-See [Exported environment bundles](testing-lanes.md#exported-environment-bundles).
+See [Exported environment bundles](../testing-lanes.md#exported-environment-bundles).
 
 ## Agent evaluation and conformance records
 
-See [Agent evaluation and conformance records](testing-lanes.md#agent-evaluation-and-conformance-records).
+See [Agent evaluation and conformance records](../testing-lanes.md#agent-evaluation-and-conformance-records).
 
 ## Frida instrumentation
 
-See [Frida instrumentation](testing-lanes.md#frida-instrumentation).
+See [Frida instrumentation](../testing-lanes.md#frida-instrumentation).
 
 ### Offline WASM artifacts
 
-See [Offline WASM artifacts](testing-lanes.md#offline-wasm-artifacts).
+See [Offline WASM artifacts](../testing-lanes.md#offline-wasm-artifacts).

docs/development/tool-design.md

@@ -178,14 +178,18 @@ does not establish another instance.
   provider-observed direct relationship set. `complete` means that set was
   returned without a known read limit; it does not claim every possible runtime
   edge. Provider and execution caveats stay in `limitations` and do not imply
-  incomplete relationship coverage. Missing coverage remains `unknown`.
+  incomplete relationship coverage. Directional `discovery` separately describes
+  whether applicable static relationships could have been missed by discovery;
+  missing discovery is unknown. Preserve paths supported by observed edges,
+  and qualify negative and shortest-path claims by discovery scope. Missing
+  relationship coverage remains `unknown`.
 - Declare process, filesystem, network, UI, and mutation effects truthfully;
   enforce the requested target and lifecycle.
 - Add limits only for real format, protocol, authority, or measured resource
   constraints. Report pagination, truncation, cancellation, and partial failure.
   An assumed agent budget is insufficient justification for a limit. Name the
   ceiling and its recovery as described in
-  [admission limits and recovery](design/limits-and-recovery.md).
+  [admission limits and recovery](../design/limits-and-recovery.md).
 
 ### Compose declared Evidence inputs
 
@@ -229,8 +233,8 @@ MCP supplies the current ledger lookup. CLI commands that advertise
 `--evidence-bundle` use one explicitly selected, authenticated bundle for the
 command's lifetime. Keep cleanup with that owner. A retained reference does not
 grant filesystem access: file selectors remain separate, explicit contracts
-where supported. See [retained Evidence inputs](mcp-contracts.md#retained-application-evidence-inputs)
-and [CLI reuse](cli.md#import-export-and-compare-evidence).
+where supported. See [retained Evidence inputs](../reference/mcp-contracts.md#retained-application-evidence-inputs)
+and [CLI reuse](../getting-started/cli.md#import-export-and-compare-evidence).
 
 ### Interpret boundary facts once
 
@@ -543,5 +547,5 @@ metadata to either adapter.
 When discoverability changes, evaluate representative broad, direct, and negative
 tasks on the intended host. Record host/model/catalog, selected tools, arguments,
 errors, retries, and task outcomes. Schema validity and keyword heuristics do not
-establish successful tool selection. See [mcp-contracts.md](mcp-contracts.md) for
+establish successful tool selection. See [mcp-contracts.md](../reference/mcp-contracts.md) for
 shipped runtime behavior.

docs/esp-image.md

@@ -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](mcp-contracts.md) for the profiles
+needed for one question. See [MCP contracts](reference/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`,

docs/getting-started/cli.md

@@ -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](javascript-artifact-reconstruction.md)
+[JavaScript artifact reconstruction](../guides/javascript/javascript-artifact-reconstruction.md)
 for results, integrity checks and coverage.
 
 The complete application Evidence can be hundreds of megabytes for a real
@@ -59,7 +59,7 @@ 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](javascript-application-workflows.md) for
+[JavaScript application workflows](../guides/javascript/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 +226,7 @@ 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](managed-code-analysis.md#cli-summary-and-saved-member-rows)
+[CLI summary and saved member rows](../guides/managed/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 +234,8 @@ 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](managed-code-analysis.md)
+[IL2CPP metadata](../il2cpp-metadata.md). NativeAOT method bodies require native
+analysis. See the [managed-code guide](../guides/managed/managed-code-analysis.md)
 for supported deployment forms, selection semantics, and coverage limits.
 
 ## SQLite snapshots
@@ -243,7 +243,7 @@ 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](sqlite-databases.md) for database/WAL identity,
+[SQLite database snapshots](../guides/data/sqlite-databases.md) for database/WAL identity,
 source-file handling and row-value semantics.
 
 ## Native analysis
@@ -256,7 +256,7 @@ 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](go-binaries.md)
+build settings, original bytes and SHA-256. See [Go binaries](../guides/native/go-binaries.md)
 for supported containers and absent or malformed metadata.
 
 Inspect a Godot PCK without running the game:
@@ -267,7 +267,7 @@ 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:
@@ -278,7 +278,7 @@ 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:
@@ -290,7 +290,7 @@ 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.
+extraction. See [wxapkg](../wxapkg.md) for layout and coverage boundaries.
 
 Inspect an ESP32-family app or bootloader image without esptool:
 
@@ -301,7 +301,7 @@ 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 +313,7 @@ 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 +322,7 @@ 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 +332,7 @@ 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:
@@ -342,7 +342,7 @@ 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
@@ -361,7 +361,7 @@ 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 +371,7 @@ 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 +385,7 @@ 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 +402,7 @@ 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 +414,7 @@ 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 +426,7 @@ 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 +437,7 @@ 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 +447,7 @@ 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 +458,7 @@ 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`:
 
@@ -474,7 +474,7 @@ 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)
@@ -486,7 +486,7 @@ 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:
 
@@ -496,7 +496,7 @@ 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).
+[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
@@ -505,10 +505,10 @@ 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](native-investigation.md).
+without returning the body inline; see [native investigation](../guides/native/native-investigation.md).
 
 Configure [Hopper or Ghidra](installation.md#hopper), the
-[IDA adapter](ida-provider.md), or [Kuna](kuna-provider.md) before analyzing a
+[IDA adapter](../providers/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 +536,11 @@ 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](mcp-contracts.md#generated-catalog) lists all CLI commands and MCP
+The [generated catalog](../reference/mcp-contracts.md#generated-catalog) lists all CLI commands and MCP
 tools. Provider-specific target support is described in the
-[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).
+[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).
 
 ## Choose a provider
 
@@ -587,13 +587,13 @@ 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](mcp-contracts.md#identity-and-discovery).
+[provider selection](../reference/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](mcp-contracts.md) for session lifecycle and
-[Ghidra first-query deadlines](mcp-contracts.md#ghidra-first-query-deadlines-and-recovery)
+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)
 for import, client timeouts and recovery.
 
 A one-shot command releases its provider session and REA runtime before it
@@ -742,6 +742,12 @@ 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`,
@@ -763,8 +769,8 @@ 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](javascript-application-workflows.md).
-MCP [retained Evidence references](mcp-contracts.md#retained-application-evidence-inputs)
+[JavaScript application workflows](../guides/javascript/javascript-application-workflows.md).
+MCP [retained Evidence references](../reference/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:
 
@@ -972,23 +978,23 @@ 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](javascript-application-workflows.md#historical-source-to-bundle-comparison)
+[source-to-bundle comparison](../guides/javascript/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](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.
-- [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](../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.
 
 Runtime requests name the target and actions. Launched targets run with your
 user permissions; consult the chosen guide for host requirements and effects.
@@ -1027,7 +1033,7 @@ 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](mcp-contracts.md#transports) for the session, `Host` header and
+[transports](../reference/mcp-contracts.md#transports) for the session, `Host` header and
 shutdown contract. Client registrations written by setup and the MCP registry
 entry keep stdio.
 
@@ -1052,7 +1058,7 @@ 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
@@ -1072,7 +1078,7 @@ 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
@@ -1097,7 +1103,7 @@ 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
@@ -1130,7 +1136,7 @@ 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
@@ -1143,7 +1149,7 @@ 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
@@ -1423,7 +1429,7 @@ 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
@@ -1439,7 +1445,7 @@ 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).
+[PE TLS and load configuration](../pe-load-config.md).
 
 ### Binary hardening
 
@@ -1449,9 +1455,9 @@ 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).
+[binary hardening](../binary-hardening.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.

docs/getting-started/client-configuration.md

@@ -43,7 +43,7 @@ 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](client-verification.md#launch-environment-verification).
+launcher; see [verification scope](../development/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
@@ -68,7 +68,7 @@ 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](client-verification.md#launch-environment-verification)
+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
@@ -83,7 +83,7 @@ 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
 
@@ -102,13 +102,15 @@ 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](mcp-contracts.md#hotcold-catalog-discovery) for
+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,
@@ -155,7 +157,7 @@ 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](mcp-contracts.md#output-schemas).
+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.
@@ -179,7 +181,7 @@ receive limits and full Evidence access still apply.
 
 Connect Fiddler Everywhere's MCP server separately for HTTP traffic debugging,
 preserving your REA client entry. See the
-[setup instructions and public skills](web-network-captures.md#fiddler-everywhere-mcp-and-public-skills).
+[setup instructions and public skills](../guides/web/web-network-captures.md#fiddler-everywhere-mcp-and-public-skills).
 
 ## VS Code
 
@@ -217,7 +219,7 @@ 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](testing.md).
+Windows remain unverified; see [native client verification](../development/testing.md).
 
 ## Claude Desktop
 
@@ -329,7 +331,7 @@ 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](mcp-contracts.md#tool-family-advertising-scope)).
+  workflow needs (see [the advertising scope contract](../reference/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
@@ -346,7 +348,7 @@ 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](mcp-contracts.md#output-schemas).
+profiles](../reference/mcp-contracts.md#output-schemas).
 
 ## Kimi Code
 
@@ -391,7 +393,7 @@ 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](mcp-contracts.md#initial-target-at-startup). Existing
+[initial-target settings](../reference/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
@@ -502,7 +504,7 @@ 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](mcp-contracts.md#compact-input-schema-profile)
+model. For schema rejection, review the [input presentation profiles](../reference/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
@@ -583,7 +585,7 @@ 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](mcp-contracts.md#schema-advertisement).
+see [schema advertisement](../reference/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
@@ -832,7 +834,7 @@ 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](testing.md#end-to-end-integration-and-golden-evidence)
+REA's optional [native client verification](../development/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.
@@ -898,7 +900,7 @@ 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](mcp-contracts.md#ghidra-first-query-deadlines-and-recovery).
+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:
 
@@ -933,7 +935,7 @@ keep the server local, and select targets and operations you are authorized to u
 
 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](client-verification.md#llamacpp) distinguishes connection
+The [verification record](../development/client-verification.md#llamacpp) distinguishes connection
 checks from model behavior and lists the tested versions.
 
 ## Other client settings

docs/getting-started/installation.md

@@ -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](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](../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)                                                                     |
 
 ## Start setup
 
@@ -374,7 +374,7 @@ 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](mcp-contracts.md#identity-and-discovery).
+[MCP discovery](../reference/mcp-contracts.md#identity-and-discovery).
 
 Select the part you want to check:
 
@@ -698,7 +698,7 @@ 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](windows-ghidra-p0.md).
+the [experimental P0 boundary](../providers/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,
@@ -1025,7 +1025,7 @@ 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](native-investigation.md#hopper-analysis-behavior).
+see [Hopper analysis behavior](../guides/native/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
@@ -1150,13 +1150,13 @@ session metadata edits leave executable bytes unchanged and are discarded on clo
 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](ghidra-dos.md), plus explicitly
-selected [raw NMOS 6502 images](raw-binary.md#nmos-6502) with a caller-supplied
+[DOS MZ executables](../providers/ghidra-dos.md), plus explicitly
+selected [raw NMOS 6502 images](../providers/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](windows-ghidra-p0.md) for verified scope and
+See the [Windows Ghidra P0 guide](../providers/windows-ghidra-p0.md) for verified scope and
 limitations.
 
 Extract Ghidra and install the JDK outside REA, then export absolute paths:
@@ -1199,7 +1199,7 @@ 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](windows-ghidra-p0.md) for provider diagnostics.
+registrations. See [Windows Ghidra P0](../providers/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 +1317,7 @@ 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](mcp-contracts.md#ghidra-first-query-deadlines-and-recovery)
+See [Ghidra first-query deadlines and recovery](../reference/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 +1370,7 @@ 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
@@ -1558,6 +1558,11 @@ 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.
+Caller and callee coverage therefore remains unknown. A single-direction query
+with known omissions remains partial and also reports the unknown project history.
+Observed call edges are still available: a path to an observed caller or callee
+can be reached, but a missing path is unknown when the project's prior analysis
+cannot establish completeness.
 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
@@ -1735,7 +1740,7 @@ 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](testing.md) for bounded
+profile identity. See [real-provider testing](../development/testing.md) for bounded
 verification workflows.
 
 ### Ghidra diagnostics and verification
@@ -1845,7 +1850,7 @@ 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](mcp-contracts.md).
+[MCP contracts](../reference/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:

docs/guides/android/adb-device-analysis.md

@@ -288,7 +288,7 @@ 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/testing.md` for the lane summary.
+complete package lifecycle; see `docs/development/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

docs/guides/android/android-analysis.md

@@ -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](installation.md#released-package-and-main) and the
+[released package boundary](../../getting-started/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](installation.md#linux-owned-process-prerequisite).
+[Linux process prerequisite](../../getting-started/installation.md#linux-owned-process-prerequisite).
 
 ## Optional package delivery
 
@@ -687,14 +687,14 @@ 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](client-configuration.md) does not include
+setup's derived [client tool timeout](../../getting-started/client-configuration.md) does not include
 this setting, so also raise the client timeout when selecting a longer
 deadline.
 

docs/guides/android/apktool-resource-analysis.md

@@ -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/testing.md` for the lane summary.
+decode. See `docs/development/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,

docs/guides/firmware/firmware-analysis.md

@@ -11,7 +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](installation.md#linux-owned-process-prerequisite).
+[Linux process prerequisite](../../getting-started/installation.md#linux-owned-process-prerequisite).
 
 ## Compare stored firmware components
 
@@ -21,7 +21,7 @@ For supported FIT and legacy uImage containers, use the built-in
 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,
+[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.
@@ -209,7 +209,7 @@ 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](ghidra-mips.md) and [RISC-V ELF](ghidra-riscv.md) lanes are separate
+[MIPS ELF](../../providers/ghidra-mips.md) and [RISC-V ELF](../../providers/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.
@@ -317,7 +317,7 @@ 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 +328,11 @@ 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 +343,7 @@ 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 +356,7 @@ 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 +366,7 @@ 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 +374,4 @@ 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).

docs/guides/javascript/electron-observation.md

@@ -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](browser-observation.md#provider-authorities).
+[CDP state limitation](../web/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

docs/guides/javascript/javascript-application-workflows.md

@@ -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](mcp-contracts.md) for filters. A handoff binds
+See [MCP contracts](../../reference/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](cli.md#import-export-and-compare-evidence).
+connection state. See [CLI Evidence reuse](../../getting-started/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](mcp-contracts.md#retained-application-evidence-inputs).
+[MCP Evidence inputs](../../reference/mcp-contracts.md#retained-application-evidence-inputs).
 
 For two operator-provided directories or ASARs, run:
 

docs/guides/javascript/javascript-artifact-reconstruction.md

@@ -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](mcp-contracts.md#integrity-record-and-continue) for the
+[MCP integrity handling](../../reference/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](mcp-contracts.md#tool-results) for delivery limits, export, and
+[MCP tool results](../../reference/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](mcp-contracts.md#progress-and-cancellation)
+waiting before receiving the reply, follow [MCP cancellation recovery](../../reference/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.
@@ -810,7 +810,7 @@ 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.

docs/guides/javascript/javascript-recovery.md

@@ -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](testing.md#javascript-source-recovery) for the focused real
+See [testing.md](../../development/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.

docs/guides/javascript/javascript-runtime-observation.md

@@ -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.

docs/guides/managed/managed-code-analysis.md

@@ -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](mcp-contracts.md#generated-catalog).
+[build-generated catalog](../../reference/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
@@ -608,13 +608,13 @@ 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](ghidra-nativeaot.md) defines
+install it or its toolchain. The [NativeAOT guide](../../providers/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](ghidra-nativeaot.md) lists what a
+parser also runs there; the [NativeAOT guide](../../providers/ghidra-nativeaot.md) lists what a
 Windows host covers.
 
 For NativeAOT analysis, preserve the selected native artifact's path and digest
@@ -623,6 +623,7 @@ 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
@@ -677,7 +678,7 @@ 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](ghidra-nativeaot.md) has its own supported boundary.
+[Ghidra NativeAOT extension](../../providers/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,
@@ -849,7 +850,7 @@ 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](windows-ghidra-p0.md)
+Windows host. The [experimental Windows Ghidra boundary](../../providers/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.
@@ -860,7 +861,7 @@ 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](testing.md#real-toolchain-verification-lanes) for prerequisites and
+[testing](../../development/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.
 

docs/guides/native/binary-diagnostics.md

@@ -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](mcp-contracts.md#tool-results).
+server `REA_MCP_MAX_RESPONSE_BYTES`. See [MCP delivery budgets](../../reference/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,

docs/guides/native/go-binaries.md

@@ -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](mcp-contracts.md), which counts both text and
+its [response transport budget](../../reference/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.

docs/guides/native/native-investigation.md

@@ -21,7 +21,7 @@ breakpoint names.
 
 ## Start with a function
 
-Choose an installed provider from [setup](installation.md#hopper). For Ghidra:
+Choose an installed provider from [setup](../../getting-started/installation.md#hopper). For Ghidra:
 
 ```bash
 rea inspect /absolute/path/to/program --provider ghidra --json
@@ -83,6 +83,9 @@ 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.
 
@@ -97,6 +100,36 @@ body are excluded. `procedure_references` returns internal and external edges;
 The reference collector's semantics participate in the analysis profile, so
 older snapshots cannot replay the former incomplete results under this profile.
 
+For a bounded handoff, request `procedure_references` with `detail: "summary"`.
+The summary retains the complete observation and reports the selected procedure,
+direction and counts. Page it with `inspect_analysis_view`, using the summary's
+`normalized_result.parent_evidence_id` and a view such as
+`{"kind":"native-procedure-references","collection":"references","source_address":"0x1234","offset":0,"limit":64}`.
+The optional exact source and target filters apply before paging. A row's
+`source_index` identifies it in the original retained collection, including
+duplicates. Endpoint `kind: "selected-procedure"` refers to the full procedure
+in the page summary; `kind: "null"` preserves the original null without asserting
+why it was unavailable. `kind: "shared"` carries an index into `items.endpoints`,
+where each other procedure object is stored once per page. Use collection
+`unresolved_calls` for paged unresolved call sites and their original reasons.
+Page coverage describes retained rows, not complete provider discovery or runtime
+execution. A 1 MiB projection allowance, also used by other bounded analysis views, can
+shorten a requested page; `byte_limited: true` and `coverage.next_offset` identify the
+continuation. A single row or summary that cannot fit returns a resource error;
+retrieve or export the complete parent Evidence. This allowance has no runtime
+override. Omit detail to receive the complete observation inline.
+
+For a one-shot CLI handoff, save the complete Evidence and its linked sources:
+
+```bash
+rea procedure-references /absolute/path/to/program my_function --provider ghidra \
+  --direction incoming --detail summary --evidence_output /absolute/path/to/references.json
+```
+
+Use `rea inspect-analysis-view` with that bundle as an `evidence-file` source to
+page it without reopening the target. This command requires a provider supporting
+`procedure_references`; Kuna currently reports that capability unavailable.
+
 Ghidra regex searches use Java Pattern semantics. If compiling or matching a
 pattern exhausts the engine's stack, REA returns a resource constraint and
 preserves the active database and annotations. Retry in literal mode or simplify
@@ -225,7 +258,7 @@ 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](mcp-contracts.md#selected-batch-decompile-results).
+decompilation: see [selected batch results](../../reference/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
@@ -252,8 +285,18 @@ The manifest reports the procedure-inventory limitations of the current call in
 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.
+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
@@ -370,7 +413,7 @@ 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
@@ -757,7 +800,7 @@ 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-application-analysis.md#dylib-load-resolution).
+  [Apple application analysis](../apple/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
@@ -1154,6 +1197,25 @@ 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
@@ -1219,15 +1281,17 @@ Install a Ghidra 12.x (>=12.1) release and the 64-bit full JDK it declares, then
 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](ghidra-dos.md), plus explicitly selected
-[raw NMOS 6502 images](raw-binary.md#nmos-6502) with a caller-supplied load address,
+executables](../../providers/ghidra-dos.md), plus explicitly selected
+[raw NMOS 6502 images](../../providers/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](windows-ghidra-p0.md) and
+handle-based path admission. See [Windows Ghidra P0](../../providers/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. Annotation text must contain no NUL or
+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
 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
@@ -1245,6 +1309,11 @@ 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:
 
@@ -1472,7 +1541,7 @@ 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](ghidra-provider.md#masked-byte-search) for mask and coverage
+[Ghidra byte search](../../providers/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;

docs/guides/native/recorded-crashes.md

@@ -2,7 +2,7 @@
 
 `inspect_recorded_crash` / `rea inspect-recorded-crash` inspect a caller-selected
 Linux ELF64 little-endian core independently of an active binary target. Apple
-`.ips` crash reports use the separate [Apple IPS](apple-ips.md) workflow. Two
+`.ips` crash reports use the separate [Apple IPS](../../apple-ips.md) workflow. Two
 architecture profiles are interpreted, x86-64 and AArch64; each binds registers
 to its own `NT_PRSTATUS` layout, and any other `e_machine` is refused as
 `unsupported_target` before note interpretation.

docs/guides/wasm/wasm-artifacts.md

@@ -122,7 +122,7 @@ To change the default across new MCP operations, set `wasm.command_timeout_ms`
 through `update_analysis_settings`. An explicit `command_timeout_ms` still wins;
 correct that argument if it caused the timeout. Runtime defaults do not insert
 omitted arguments into Evidence parameters. See the
-[settings design](design/limits-and-recovery.md#precedence-and-lifetime).
+[settings design](../../design/limits-and-recovery.md#precedence-and-lifetime).
 
 For example, `rea inspect-wasm-artifact /artifacts/module.wasm
 --command-timeout-ms 60000 --format json` uses a 60-second per-command deadline;
@@ -170,7 +170,7 @@ Candidates are caller-selected files; their identity does not imply validation.
 Both CLI and MCP use the same typed port and application service. MCP publishes
 SDK-compatible schemas and records Evidence for `get_evidence_bundle` readback.
 See [WABT provenance](https://github.com/morluto/rea/blob/main/third_party/wabt/README.md) and
-[testing](testing.md#offline-wasm-artifacts) for real-tool verification.
+[testing](../../development/testing.md#offline-wasm-artifacts) for real-tool verification.
 
 ## Compare core-module interfaces
 

docs/guides/web/browser-observation.md

@@ -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](electron-observation.md).
+Electron `file://` pages use a separate provider and target boundary; see [electron-observation.md](../javascript/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-runtime-reconciliation.md).
+[JavaScript static/runtime reconciliation](../javascript/javascript-runtime-reconciliation.md).
 
 ## Start a browser
 

docs/guides/web/web-network-captures.md

@@ -599,7 +599,7 @@ selected response bodies or header values: each network transaction is then
 one record, in request order, and the result names
 `parent_operation: "capture_browser_scenario"` with an empty `artifact`, since
 a scenario records no file. See
-[agent environments](agent-environments.md#from-a-browser-scenario).
+[agent environments](../../agent-environments.md#from-a-browser-scenario).
 
 ```json
 {
@@ -1084,7 +1084,7 @@ capture with many read-only paths yields a correspondingly larger state result.
 The view performs no network activity and serves nothing; `rea environment-serve`
 derives it from the capture at startup, serves read tools and the served write
 plans from it and loads replacement states through the AgentEnv data plane, as
-[serve from the state](agent-environments.md#serve-from-the-state) describes.
+[serve from the state](../../agent-environments.md#serve-from-the-state) describes.
 
 ## Environment coverage
 
@@ -1105,7 +1105,7 @@ an environment whose served catalog exceeds the discovery budget, or whose
 state exceeds what `data/add` loads, serves replay, and `rea environment-build`
 then reports `coverage: null`; otherwise the build prints this summary as its
 `coverage`. See
-[Build a bundle in one step](agent-environments.md#build-a-bundle-in-one-step)
+[Build a bundle in one step](../../agent-environments.md#build-a-bundle-in-one-step)
 for the hint per reason.
 
 ## Resource and lifecycle boundaries
@@ -1155,7 +1155,7 @@ host memory or `NODE_OPTIONS` does not raise the old-generation heap. Update
 `capture.decoder_old_generation_mib` through MCP, or set
 `REA_CAPTURE_DECODER_OLD_GENERATION_MIB` before starting a new REA process.
 Retry after owned cleanup completes; the update does not release resources.
-See the [settings design](design/limits-and-recovery.md#failure-and-retry).
+See the [settings design](../../design/limits-and-recovery.md#failure-and-retry).
 Record selection happens after complete decoding and does not reduce that
 workload. Use a smaller capture exported by its producer or another decoder
 with sufficient capacity, retaining the original for provenance. Subsets do

docs/guides/web/website-module-trace.md

@@ -91,7 +91,7 @@ launches it without one. On hosts that cannot provide one, such as root in a
 container, `REA_BROWSER_NO_SANDBOX=true` launches it without the sandbox; the
 variable does not enable an REA security boundary.
 
-See [testing](testing.md) for the native loading oracle and CLI/MCP real lane.
+See [testing](../../development/testing.md) for the native loading oracle and CLI/MCP real lane.
 
 The selected local source filename supplies the parser grammar. JavaScript files
 retain native dynamic imports even in relational expressions; TypeScript files

docs/il2cpp-metadata.md

@@ -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](cli.md#run-a-command). Compact delivery requires
+in [CLI and Evidence](getting-started/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`](installation.md) so Ghidra names every IL2CPP method
+[`REA_GHIDRA_SEED_FILE`](getting-started/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](mcp-contracts.md); a complete report within the
+[response transport budget](reference/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`](installation.md); use the
-  [native workflow](native-investigation.md) for native code.
+  file for [`REA_GHIDRA_SEED_FILE`](getting-started/installation.md); use the
+  [native workflow](guides/native/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

docs/index.md

@@ -41,37 +41,33 @@ 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](./installation.md) for requirements and configuration.
+See [installation and setup](getting-started/installation.md) for requirements and configuration.
 
-For runtime instrumentation, see the [Frida guide](./frida-instrumentation.md).
+For runtime instrumentation, see the [Frida guide](guides/runtime/frida-instrumentation.md).
 
 ## Choose a guide
 
-| 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), [Binary hardening](binary-hardening.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), [wxapkg](wxapkg.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)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
-| Capture a Linux desktop application in use          | [Desktop application capture](desktop-application-capture.md)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
-| Read a captured application's state                 | [Desktop application state](desktop-application-state.md)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
-| Export a captured application as an environment     | [Desktop application export](desktop-application-export.md)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
-| Write and validate a task for an exported app       | [Desktop application tasks](desktop-application-tasks.md)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
-| Drive a computer while building an environment      | [Desktop build computer](desktop-build-computer.md)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
-| Capture, export and witness a built environment     | [Building and witnessing](desktop-build-witness.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)                                                                                                                                                                                                                                                                                                                                                                                                                                              |
+The [documentation directory](README.md) lists every guide by domain.
 
-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.
+| 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.
 
 ![REA inspecting a native binary in Hopper](./assets/rea-hopper-analysis.png)

docs/kuna-provider.md

@@ -147,6 +147,7 @@ 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.
@@ -172,7 +173,7 @@ 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](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](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.
 
 ## Verify with a real Kuna
 
@@ -183,7 +184,7 @@ 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. See [testing](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. 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.
 
 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.
 

docs/migrations/migration-6.2.md

@@ -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](mcp-contracts.md#tool-results).
+[`tools/list` and the result guide](../reference/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](cli.md#save-and-reuse-analysis-snapshots).
+[snapshot usage](../getting-started/cli.md#save-and-reuse-analysis-snapshots).
 
 Artifact inventory nodes identify content bytes. Path-specific role and
 permissions now belong to each occurrence:

docs/native-function-matching.md

@@ -95,7 +95,8 @@ 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. Page coverage covers selected retained facts. Function identity binds
+selection. Default function rows include member limitations; an explicit `fields`
+selection can omit them. 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.

docs/providers/ghidra-mips.md

@@ -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](installation.md#ghidra)). The refusal
+declaration beyond EOF ([installation](../getting-started/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

docs/providers/ghidra-nativeaot.md

@@ -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`](../licenses/nativeaot-parser-MIT.txt).
+[`licenses/nativeaot-parser-MIT.txt`](https://github.com/morluto/rea/blob/main/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](testing.md#optional-nativeaot-ghidra-analysis).
+See [the dedicated lane](../development/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

docs/providers/ghidra-provider.md

@@ -5,7 +5,7 @@ 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.
 Executable bytes remain unchanged.
 
-An opt-in [owned Program checkpoint](installation.md#automatically-checkpoint-an-owned-ghidra-program)
+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
@@ -14,16 +14,16 @@ keeps one stable generation through its first save; later saved states bind thei
 content digest in profile identity. Restoration does not turn prior
 database state into a fresh discovery. The default remains ephemeral.
 
-Use [installation](installation.md#ghidra) for supported hosts, prerequisites,
+Use [installation](../getting-started/installation.md#ghidra) for supported hosts, prerequisites,
 configuration, startup deadlines, resource controls, and cleanup recovery.
-[Linux Ghidra launches](installation.md#linux-owned-process-prerequisite) also
+[Linux Ghidra launches](../getting-started/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](installation.md#released-package-and-main) when using npm.
+[release boundary](../getting-started/installation.md#released-package-and-main) when using npm.
 
-See [import language and analysis seeds](installation.md#ghidra-import-language-and-analysis-seeds)
+See [import language and analysis seeds](../getting-started/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 +52,7 @@ 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](mcp-contracts.md#identity-and-discovery). One deep
+[MCP contracts](../reference/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.
@@ -89,6 +89,13 @@ 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:
@@ -133,6 +140,11 @@ 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`.
@@ -264,9 +276,21 @@ 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
@@ -335,10 +359,17 @@ must be constrained.
 
 Optional `start` and `end` addresses are inclusive and select one address space.
 A match must end at or before `end`, so `end` set inside a match excludes it.
-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.
+Without bounds, loaded non-overlay memory blocks are eligible, in Ghidra address
+order, including across adjacent initialized blocks. Blocks that are not loaded
+(file parts such as `.symtab`) are listed in `searched.skipped_not_loaded`;
+loaded overlay blocks are listed separately in `searched.skipped_overlays`.
+Neither is searched by default; pass `start` or `end` in its address space to
+search it. A block that is both unloaded and an overlay is listed once under
+`skipped_not_loaded`.
+The separate overlay field changes the byte-search result contract and the
+Ghidra analysis profile. Refresh cached MCP schemas; snapshots from the older
+profile are not replayed. Previously exported Evidence remains importable as
+historical data with its original result shape.
 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

docs/providers/ghidra-riscv.md

@@ -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](installation.md#ghidra).
+[installation](../getting-started/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

docs/providers/ida-provider.md

@@ -245,7 +245,7 @@ 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](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](../development/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.
 

docs/providers/jeb-analysis.md

@@ -68,7 +68,7 @@ All four preserve target-file bytes. `open_jeb_project` selects or creates an en
 - 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.
 
-Real-engine verification lives in the JEB lane described in [testing.md](testing.md); mock transport tests do not establish real-engine compatibility.
+Real-engine verification lives in the JEB lane described in [testing.md](../development/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

docs/providers/raw-binary.md

@@ -1,7 +1,7 @@
 # Headerless raw-binary analysis with Ghidra
 
 Headerless images are covered here. GameCube/Wii DOL images have a header and
-use their own format selection; see [GameCube DOL analysis](ghidra-dol.md).
+use their own format selection; see [GameCube DOL analysis](../ghidra-dol.md).
 
 REA admits a headerless executable when the caller supplies the CPU family and
 the address where file offset 0 should be mapped. That interpretation is not

docs/providers/windows-ghidra-p0.md

@@ -1,7 +1,7 @@
 # Windows Ghidra P0
 
 This guide describes repository main. npm 4.1.0 includes the Windows
-native bundle; check the [release boundary](installation.md#released-package-and-main)
+native bundle; check the [release boundary](../getting-started/installation.md#released-package-and-main)
 before applying these instructions to an older published package.
 Native x86 (32-bit) PE support is available on repository main; npm releases
 through 5.0.0 admit x86-64 PE targets on Windows.
@@ -26,7 +26,7 @@ Loaded memory reads and file offsets preserve Ghidra's observed source mappings.
 PE load-image inspection returns an explicit unsupported attestation status.
 Independent verification covers admitted DOS MZ, explicit COM, explicit
 [raw-binary imports](raw-binary.md), and explicit
-[GameCube DOL images](ghidra-dol.md) on their supported hosts, including the
+[GameCube DOL images](../ghidra-dol.md) on their supported hosts, including the
 admitted DOS MZ and raw NMOS 6502 mappings on Windows. Windows P0 admission remains limited
 to native PE, DOS MZ, and raw NMOS 6502 images; explicit COM is not admitted. For x64 PE
 NativeAOT RTR 9.1, the read-only snapshot parser can report metadata through

docs/readme/README_ar.md

@@ -10,7 +10,7 @@
 **وجدت ميزة تعجبك؟ افهم طريقة عملها حتى مستوى الشيفرة الثنائية.**
 
 [![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)](../mcp-contracts.md#generated-catalog)
+[![MCP tool catalog](https://img.shields.io/badge/MCP-tool_catalog-5c4ee5?style=flat-square)](../reference/mcp-contracts.md#generated-catalog)
 [![Node.js requirements](https://img.shields.io/badge/Node.js-requirements-339933?style=flat-square&logo=nodedotjs&logoColor=white)](#current-status)
 [![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)
@@ -80,7 +80,7 @@ npx rea-agents setup
 
 اختر الوكلاء، وراجع التغييرات المقترحة، ثم وافق عليها. يضيف الإعداد خادم MCP الخاص بـ REA وتعليمات سير العمل المطابقة، مع الاحتفاظ بنسخ احتياطية من الإعدادات الموجودة. أعد تشغيل وكيلك بعد ذلك.
 
-يدعم الإعداد Claude Code وCodex وCursor وGemini CLI وGrok Build و[وكلاء آخرين](../installation.md#supported-agents). راجع [التثبيت والإعداد](../installation.md) لتهيئة موفّري التحليل وتسجيل MCP يدويًا.
+يدعم الإعداد Claude Code وCodex وCursor وGemini CLI وGrok Build و[وكلاء آخرين](../getting-started/installation.md#supported-agents). راجع [التثبيت والإعداد](../getting-started/installation.md) لتهيئة موفّري التحليل وتسجيل MCP يدويًا.
 
 يستخدم MCP مخططات إدخال مختصرة افتراضيًا. للحصول على إرشادات الحقول الكاملة وتفاصيل التحقق المتداخل، اضبط `REA_MCP_INPUT_SCHEMA_PROFILE=full` في تسجيل MCP. يحتفظ الخياران بجميع الأدوات والتحقق القياسي نفسه على الخادم؛ راجع دليل عقود MCP.
 
@@ -109,7 +109,7 @@ npm install --global rea-agents
 rea --help
 ```
 
-لتحليل الشيفرة الأصلية، هيّئ موفّرًا أولًا. راجع [دليل CLI وEvidence](../cli.md) لأوامر تحليل الشيفرة الأصلية، واختيار الموفّر، واللقطات، والاستخدام في السكربتات.
+لتحليل الشيفرة الأصلية، هيّئ موفّرًا أولًا. راجع [دليل CLI وEvidence](../getting-started/cli.md) لأوامر تحليل الشيفرة الأصلية، واختيار الموفّر، واللقطات، والاستخدام في السكربتات.
 
 ### تحديث REA
 
@@ -151,45 +151,45 @@ npx rea-agents@latest setup
 
 يتطلب REA إصدار Node.js 22.x (>=22.23.4) أو 24.x (>=24.22.1) أو 26+ (>=26.12.1)، إضافة إلى npm. تعتمد الأدوات الإضافية والأنظمة المضيفة المدعومة على الهدف:
 
-| الهدف                           | ما يعيده REA                                                                                               | المتطلبات والدليل                                                                                                                    |
-| ------------------------------- | ---------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------ |
-| الملفات الثنائية للشيفرة الأصلية | شيفرة شبه برمجية، وتعليمات تجميع، وسلاسل نصية، ورموز، واستدعاءات، ومراجع                                    | Hopper أو Ghidra أو IDA أو Kuna؛ [تحليل الشيفرة الأصلية](../native-investigation.md)                                                  |
-| بنية ELF دون تشغيل              | الأقسام والمقاطع والرموز ومعلومات إعادة التموضع الأصلية، وآليات الحماية المحتملة المستدلّ عليها بالفحص الثابت | pwntools يوفّره المستدعي على Linux x64؛ [تشخيص الملفات الثنائية](../binary-diagnostics.md)                                            |
-| PE certificates                 | Authenticode WIN_CERTIFICATE entries and PKCS#7 signer/X.509 identity fields                               | Built-in static PE inspection; [PE certificates](../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](../pe-imports.md)                                                                        |
-| شيفرة EVM البايتية              | محددات التوجيه، وإزاحات البايتات، والمعاملات المستنتجة، وقابلية تغيير الحالة                                | مدخل محلي يحمل بايتات خامًا أو تمثيلًا سداسيًا عشريًا على Linux x64؛ [دليل EVM دون تشغيل](../evm-bytecode.md)                             |
-| Rust binaries                   | Embedded cargo-auditable dependency list                                                                   | [Rust binaries](../rust-binaries.md)                                                                                                 |
-| ELF notes                       | PT_NOTE/SHT_NOTE owners, types, GNU build-id and ABI-tag fields                                            | Built-in static ELF inspection; [ELF notes](../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](../binary-hardening.md)                                                        |
-| Linux kernel modules            | .modinfo keys, __versions CRCs, this_module presence, and signature trailer                                | Built-in static ELF inspection; [kernel modules](../kernel-modules.md)                                                               |
-| Erlang BEAM                     | IFF chunks, atoms, exports, and tables                                                                     | Built-in static BEAM inspection; [Erlang BEAM](../erlang-beam.md)                                                                    |
-| Apple IPS crashes               | .ips metadata, threads, images, registers and crash classes                                                | Built-in static JSON inspection; [Apple IPS](../apple-ips.md)                                                                        |
-| أعطال Linux المسجّلة             | سجلات note الخام، ومسجّلات المعالج/الإشارات لكل خيط مسجّل، وترشيحات اختيارية لخرائط الذاكرة                     | pwntools يوفّره المستدعي على Linux x64؛ GDB/pwndbg اختياريان؛ [الأعطال المسجّلة](../recorded-crashes.md)                                |
-| تثبيتات سطح المكتب              | عائلات وقت التشغيل، والملفات الداعمة، وعلامات المكونات، والخطوات التالية                                     | فحص محدود للملفات والترويسات；[تطبيقات سطح المكتب](../desktop-applications.md)                                                       |
-| JavaScript / Electron           | الوحدات، وعمليات الاستيراد، وخرائط المصدر، والمسارات، وIPC، وعلاقات إضافات الشيفرة الأصلية                    | Node.js وnpm؛ [تحليل التطبيقات](../javascript-application-workflows.md); Linux: procps `ps`                                          |
-| المواقع                         | بنية الصفحة، والسكربتات، وملاحظات الشبكة، ولقطات الشاشة المطلوبة                                            | متصفح من عائلة Chrome؛ [تحليل المتصفح](../browser-observation.md)                                                                    |
-| تسجيلات الشبكة المحفوظة          | الطلبات، والاستجابات، ومحتويات الحمولة المتاحة، ومواضعها في المصدر                                          | HAR / Fiddler Everywhere SAZ؛ وmitmdump على Linux لتسجيلات mitmproxy بصيغتها الأصلية؛ [دليل تسجيلات الشبكة](../web-network-captures.md) |
-| التقاط الحزم                    | نقاط النهاية وDNS وTLS SNI وتوزيع البروتوكولات وطلبات HTTP                                                  | tshark وcapinfos يوفّرهما المُستدعي؛ [دليل pcap](../pcap-analysis.md)                                                                  |
-| تجميعات .NET                    | البيانات الوصفية، وتعليمات CIL، واعتماديات الشيفرة الأصلية المعلنة، ومقارنات البناء                         | فحص ثابت؛ [دليل الشيفرة المُدارة](../managed-code-analysis.md)                                                                        |
-| PyInstaller                     | CArchive, PYZ, Python bytecode                                                                             | Static inspection; [Python packaged applications](../python-packaged-applications.md)                                                |
-| حزم Android APK                 | تصريحات ملف manifest، والأصناف، والدوال الناتجة عن فك الترجمة، والمراجع                                     | JADX دون واجهة رسومية وJDK كامل على Linux/macOS/Windows x64؛ [دليل Android](../android-analysis.md)                                  |
-| أجهزة Android                   | الأجهزة والحزم والعمليات والسجلات والدامبات ولقطات الشاشة ونقل APK/الملفات                                   | adb يوفّره المُستدعي (محاكي أو جهاز)؛ [دليل ADB](../adb-device-analysis.md)                                                            |
-| مشاريع JEB                      | وحدات المشروع من المحرك وبصمات المصنّفات والكود الزائف للأنواع/الدوال                                        | عميل JEB يبدأه المُستدعي ويقدّم MCP، ويُختار عبر REA_JEB_MCP_URL؛ [دليل JEB](../jeb-analysis.md)                                        |
-| موارد Android                   | البيان المفكوك الترميز وجداول السلاسل واللغات وحقائق الإصدار                                                 | مُشغّل Apktool يوفّره المُستدعي؛ [دليل الموارد](../apktool-resource-analysis.md)                                                         |
-| تطبيقات Flutter                 | بصمة لقطة Dart وهشوش المكتبات لكل ABI وأصل بناء المحرك                                                     | لا شيء (تحليل APK ساكن)؛ [دليل Flutter](../flutter-analysis.md)                                                                       |
-| البرامج الثابتة                 | المناطق، ونتائج الاستخراج، وما يُمرّر إلى تحليل الشيفرة الأصلية                                                | Binwalk / Unblob على Linux؛ [دليل البرامج الثابتة](../firmware-analysis.md)                                                          |
-| الحزم المسجلة                   | حقول مختارة وقيم متكررة ومرشحات وقواعد فك الترميز                                                          | Linux: TShark 4.x + prlimit; [دليل التقاط الحزم](../packet-captures.md)                                                              |
-| الإشارات المنطقية المسجلة        | تعليقات مفكك الترميز ونطاقات العينات ومعلومات التشخيص                                                      | Linux: sigrok-cli 0.7.2 + prlimit; [دليل الإشارات](../signal-recordings.md)                                                           |
-| الحزم والموارد                  | قوائم الملفات، والبصمات، وملفات plist، وبنية حزم Apple، والموارد المستخرجة                                 | [دليل تحليل الملفات وJavaScript](../javascript-artifact-reconstruction.md)، [تطبيقات Apple](../apple-application-analysis.md)        |
-| سلوك العمليات                   | مخرجات الطرفية، والتفاعلات، وملاحظات الخروج ونظام الملفات، ومقارنات التشغيل                                  | Linux/macOS مع PTY أصلي؛ [تسجيل سلوك العمليات](../process-capture.md)                                                                |
-| ملفات Go الثنائية               | إصدار المترجم المضمّن والوحدات والاستبدالات وإعدادات البناء                                                   | فحص ثابت مدمج ELF/PE/thin Mach-O; لا يتطلب تثبيت Go                                                                                   |
-| قواعد بيانات SQLite             | الجداول والأعمدة والفهارس والعروض والمشغلات وصفوف مختارة من الجداول العادية                                  | لقطة محلية لقاعدة البيانات/WAL؛ Node.js 24.x >=24.15 أو 26+ مع حدود SQLite الأصلية                                                    |
-| كائنات شيفرة GPU                | أهداف CUDA/HIP ومعاملات وموارد النوى المختارة ونص PTX المحفوظ                                               | فحص ثابت مدمج ELF/PE/fatbin/CUBIN/PTX; [GPU](../gpu-code-objects.md)                                                                 |
-| ملفات النماذج                   | بيانات GGUF / safetensors الوصفية وتصريحات الموترات والمجاميع المشتقة                                      | فحص الترويسات؛ بصمة الملف الكامل اختيارية; [GGUF / safetensors](../model-artifacts.md)                                               |
-| بيانات IL2CPP الوصفية           | صور التجميعات وأسماء الأنواع والدوال ونطاقات الفهارس في Unity global-metadata.dat                           | فك ثابت للإصدارات 24 و27 و29 و31 و39؛ لا يتطلب Unity                                                                                   |
-| Godot PCK                       | جرد الأرشيف واستخراجه وحقائق الترويسات والأدلة الأصلية وهوية المحتوى المختار                                  | الصيغ الثابتة 2 و3 و4؛ لا يتطلب Godot                                                                                                 |
-| ملفات WASM                      | التحقق والأقسام وأشكال WAT الدقيقة للاستيراد والتصدير وWAT المفكوك                                           | يوفّره المستخدم WABT 1.0.42; `inspect_wasm_artifact`                                                                                  |
-| توقيعات APK                     | الموقّعون v1/v2/v3/v3.1 وبصمات الشهادات وتدوير المفاتيح واتساق الملخصات داخليًا                              | فحص ثابت مدمج; `inspect_apk_signature`                                                                                               |
+| الهدف                           | ما يعيده REA                                                                                               | المتطلبات والدليل                                                                                                                                            |
+| ------------------------------- | ---------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| الملفات الثنائية للشيفرة الأصلية | شيفرة شبه برمجية، وتعليمات تجميع، وسلاسل نصية، ورموز، واستدعاءات، ومراجع                                    | Hopper أو Ghidra أو IDA أو Kuna؛ [تحليل الشيفرة الأصلية](../guides/native/native-investigation.md)                                                            |
+| بنية ELF دون تشغيل              | الأقسام والمقاطع والرموز ومعلومات إعادة التموضع الأصلية، وآليات الحماية المحتملة المستدلّ عليها بالفحص الثابت | pwntools يوفّره المستدعي على Linux x64؛ [تشخيص الملفات الثنائية](../guides/native/binary-diagnostics.md)                                                      |
+| PE certificates                 | Authenticode WIN_CERTIFICATE entries and PKCS#7 signer/X.509 identity fields                               | Built-in static PE inspection; [PE certificates](../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](../pe-imports.md)                                                                                                |
+| شيفرة EVM البايتية              | محددات التوجيه، وإزاحات البايتات، والمعاملات المستنتجة، وقابلية تغيير الحالة                                | مدخل محلي يحمل بايتات خامًا أو تمثيلًا سداسيًا عشريًا على Linux x64؛ [دليل EVM دون تشغيل](../guides/evm/evm-bytecode.md)                                          |
+| Rust binaries                   | Embedded cargo-auditable dependency list                                                                   | [Rust binaries](../rust-binaries.md)                                                                                                                         |
+| ELF notes                       | PT_NOTE/SHT_NOTE owners, types, GNU build-id and ABI-tag fields                                            | Built-in static ELF inspection; [ELF notes](../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](../binary-hardening.md)                                                                                |
+| Linux kernel modules            | .modinfo keys, __versions CRCs, this_module presence, and signature trailer                                | Built-in static ELF inspection; [kernel modules](../kernel-modules.md)                                                                                       |
+| Erlang BEAM                     | IFF chunks, atoms, exports, and tables                                                                     | Built-in static BEAM inspection; [Erlang BEAM](../erlang-beam.md)                                                                                            |
+| Apple IPS crashes               | .ips metadata, threads, images, registers and crash classes                                                | Built-in static JSON inspection; [Apple IPS](../apple-ips.md)                                                                                                |
+| أعطال Linux المسجّلة             | سجلات note الخام، ومسجّلات المعالج/الإشارات لكل خيط مسجّل، وترشيحات اختيارية لخرائط الذاكرة                     | pwntools يوفّره المستدعي على Linux x64؛ GDB/pwndbg اختياريان؛ [الأعطال المسجّلة](../guides/native/recorded-crashes.md)                                          |
+| تثبيتات سطح المكتب              | عائلات وقت التشغيل، والملفات الداعمة، وعلامات المكونات، والخطوات التالية                                     | فحص محدود للملفات والترويسات；[تطبيقات سطح المكتب](../desktop-applications.md)                                                                               |
+| JavaScript / Electron           | الوحدات، وعمليات الاستيراد، وخرائط المصدر، والمسارات، وIPC، وعلاقات إضافات الشيفرة الأصلية                    | Node.js وnpm؛ [تحليل التطبيقات](../guides/javascript/javascript-application-workflows.md); Linux: procps `ps`                                                |
+| المواقع                         | بنية الصفحة، والسكربتات، وملاحظات الشبكة، ولقطات الشاشة المطلوبة                                            | متصفح من عائلة Chrome؛ [تحليل المتصفح](../guides/web/browser-observation.md)                                                                                 |
+| تسجيلات الشبكة المحفوظة          | الطلبات، والاستجابات، ومحتويات الحمولة المتاحة، ومواضعها في المصدر                                          | HAR / Fiddler Everywhere SAZ؛ وmitmdump على Linux لتسجيلات mitmproxy بصيغتها الأصلية؛ [دليل تسجيلات الشبكة](../guides/web/web-network-captures.md)              |
+| التقاط الحزم                    | نقاط النهاية وDNS وTLS SNI وتوزيع البروتوكولات وطلبات HTTP                                                  | tshark وcapinfos يوفّرهما المُستدعي؛ [دليل pcap](../guides/data/pcap-analysis.md)                                                                              |
+| تجميعات .NET                    | البيانات الوصفية، وتعليمات CIL، واعتماديات الشيفرة الأصلية المعلنة، ومقارنات البناء                         | فحص ثابت؛ [دليل الشيفرة المُدارة](../guides/managed/managed-code-analysis.md)                                                                                 |
+| PyInstaller                     | CArchive, PYZ, Python bytecode                                                                             | Static inspection; [Python packaged applications](../python-packaged-applications.md)                                                                        |
+| حزم Android APK                 | تصريحات ملف manifest، والأصناف، والدوال الناتجة عن فك الترجمة، والمراجع                                     | JADX دون واجهة رسومية وJDK كامل على Linux/macOS/Windows x64؛ [دليل Android](../guides/android/android-analysis.md)                                           |
+| أجهزة Android                   | الأجهزة والحزم والعمليات والسجلات والدامبات ولقطات الشاشة ونقل APK/الملفات                                   | adb يوفّره المُستدعي (محاكي أو جهاز)؛ [دليل ADB](../guides/android/adb-device-analysis.md)                                                                     |
+| مشاريع JEB                      | وحدات المشروع من المحرك وبصمات المصنّفات والكود الزائف للأنواع/الدوال                                        | عميل JEB يبدأه المُستدعي ويقدّم MCP، ويُختار عبر REA_JEB_MCP_URL؛ [دليل JEB](../providers/jeb-analysis.md)                                                      |
+| موارد Android                   | البيان المفكوك الترميز وجداول السلاسل واللغات وحقائق الإصدار                                                 | مُشغّل Apktool يوفّره المُستدعي؛ [دليل الموارد](../guides/android/apktool-resource-analysis.md)                                                                  |
+| تطبيقات Flutter                 | بصمة لقطة Dart وهشوش المكتبات لكل ABI وأصل بناء المحرك                                                     | لا شيء (تحليل APK ساكن)؛ [دليل Flutter](../guides/android/flutter-analysis.md)                                                                                |
+| البرامج الثابتة                 | المناطق، ونتائج الاستخراج، وما يُمرّر إلى تحليل الشيفرة الأصلية                                                | Binwalk / Unblob على Linux؛ [دليل البرامج الثابتة](../guides/firmware/firmware-analysis.md)                                                                  |
+| الحزم المسجلة                   | حقول مختارة وقيم متكررة ومرشحات وقواعد فك الترميز                                                          | Linux: TShark 4.x + prlimit; [دليل التقاط الحزم](../guides/data/packet-captures.md)                                                                          |
+| الإشارات المنطقية المسجلة        | تعليقات مفكك الترميز ونطاقات العينات ومعلومات التشخيص                                                      | Linux: sigrok-cli 0.7.2 + prlimit; [دليل الإشارات](../guides/signals/signal-recordings.md)                                                                    |
+| الحزم والموارد                  | قوائم الملفات، والبصمات، وملفات plist، وبنية حزم Apple، والموارد المستخرجة                                 | [دليل تحليل الملفات وJavaScript](../guides/javascript/javascript-artifact-reconstruction.md)، [تطبيقات Apple](../guides/apple/apple-application-analysis.md) |
+| سلوك العمليات                   | مخرجات الطرفية، والتفاعلات، وملاحظات الخروج ونظام الملفات، ومقارنات التشغيل                                  | Linux/macOS مع PTY أصلي؛ [تسجيل سلوك العمليات](../guides/runtime/process-capture.md)                                                                         |
+| ملفات Go الثنائية               | إصدار المترجم المضمّن والوحدات والاستبدالات وإعدادات البناء                                                   | فحص ثابت مدمج ELF/PE/thin Mach-O; لا يتطلب تثبيت Go                                                                                                           |
+| قواعد بيانات SQLite             | الجداول والأعمدة والفهارس والعروض والمشغلات وصفوف مختارة من الجداول العادية                                  | لقطة محلية لقاعدة البيانات/WAL؛ Node.js 24.x >=24.15 أو 26+ مع حدود SQLite الأصلية                                                                            |
+| كائنات شيفرة GPU                | أهداف CUDA/HIP ومعاملات وموارد النوى المختارة ونص PTX المحفوظ                                               | فحص ثابت مدمج ELF/PE/fatbin/CUBIN/PTX; [GPU](../gpu-code-objects.md)                                                                                         |
+| ملفات النماذج                   | بيانات GGUF / safetensors الوصفية وتصريحات الموترات والمجاميع المشتقة                                      | فحص الترويسات؛ بصمة الملف الكامل اختيارية; [GGUF / safetensors](../model-artifacts.md)                                                                       |
+| بيانات IL2CPP الوصفية           | صور التجميعات وأسماء الأنواع والدوال ونطاقات الفهارس في Unity global-metadata.dat                           | فك ثابت للإصدارات 24 و27 و29 و31 و39؛ لا يتطلب Unity                                                                                                           |
+| Godot PCK                       | جرد الأرشيف واستخراجه وحقائق الترويسات والأدلة الأصلية وهوية المحتوى المختار                                  | الصيغ الثابتة 2 و3 و4؛ لا يتطلب Godot                                                                                                                         |
+| ملفات WASM                      | التحقق والأقسام وأشكال WAT الدقيقة للاستيراد والتصدير وWAT المفكوك                                           | يوفّره المستخدم WABT 1.0.42; `inspect_wasm_artifact`                                                                                                          |
+| توقيعات APK                     | الموقّعون v1/v2/v3/v3.1 وبصمات الشهادات وتدوير المفاتيح واتساق الملخصات داخليًا                              | فحص ثابت مدمج; `inspect_apk_signature`                                                                                                                       |
 
 يقرأ الفحص الثابت لـ JavaScript و.NET الملفات المقدّمة دون تشغيل التطبيق. يشغّل التسجيل أثناء التنفيذ الهدف المحدد أو يتفاعل معه بصلاحيات مستخدمك؛ ويشرح كل دليل للتسجيل أثناء التنفيذ آثاره.
 
@@ -197,7 +197,7 @@ npx rea-agents@latest setup
 
 للملفات الثنائية الكبيرة، ارفع مهلة بدء الموفّر باستخدام `REA_GHIDRA_STARTUP_TIMEOUT_MS` أو `REA_HOPPER_STARTUP_TIMEOUT_MS`.
 
-تختلف صيغ ملفات الشيفرة الأصلية والأنظمة المضيفة المدعومة باختلاف الموفّر. راجع [إعداد Hopper وGhidra](../installation.md#hopper)، و[دليل IDA](../ida-provider.md)، [Kuna](../kuna-provider.md)، و[دعم Ghidra التجريبي على Windows](../windows-ghidra-p0.md). يدعم Ghidra أيضًا [تحليل DOS ذي 16 بت](../ghidra-dos.md). لاختيار الموفّر، راجع [دليل CLI](../cli.md#choose-a-provider). تحقّق من [توفر الميزات في الإصدارات](../installation.md#released-package-and-main) للميزات المضافة بعد أحدث إصدار على npm.
+تختلف صيغ ملفات الشيفرة الأصلية والأنظمة المضيفة المدعومة باختلاف الموفّر. راجع [إعداد Hopper وGhidra](../getting-started/installation.md#hopper)، و[دليل IDA](../providers/ida-provider.md)، [Kuna](../kuna-provider.md)، و[دعم Ghidra التجريبي على Windows](../providers/windows-ghidra-p0.md). يدعم Ghidra أيضًا [تحليل DOS ذي 16 بت](../providers/ghidra-dos.md). لاختيار الموفّر، راجع [دليل CLI](../getting-started/cli.md#choose-a-provider). تحقّق من [توفر الميزات في الإصدارات](../getting-started/installation.md#released-package-and-main) للميزات المضافة بعد أحدث إصدار على npm.
 
 ## دراسات الحالة
 
@@ -278,28 +278,28 @@ agent-env run ./my-env
 <details>
 <summary><strong>أي وكلاء يمكنهم استخدام REA؟</strong></summary>
 
-أي وكيل يدعم خوادم MCP المحلية. يهيّئ الإعداد [الوكلاء المدعومين](../installation.md#supported-agents)؛ ويمكن للعملاء الآخرين استخدام [تسجيل MCP يدويًا](../installation.md#mcp-registry).
+أي وكيل يدعم خوادم MCP المحلية. يهيّئ الإعداد [الوكلاء المدعومين](../getting-started/installation.md#supported-agents)؛ ويمكن للعملاء الآخرين استخدام [تسجيل MCP يدويًا](../getting-started/installation.md#mcp-registry).
 
 </details>
 
 <details>
 <summary><strong>هل أحتاج إلى Hopper أو Ghidra أو IDA أو Kuna؟</strong></summary>
 
-يستخدم تحليل الشيفرة الأصلية المتعمق أحدها. يعمل الفحص الثابت لـ JavaScript و.NET دون محرك لتحليل الشيفرة الأصلية. يستطيع الإعداد تثبيت Hopper بعد الموافقة؛ أما Ghidra وIDA وKuna فتستخدم تثبيتاتك الموجودة. راجع [إعداد الموفّرين](../installation.md#hopper).
+يستخدم تحليل الشيفرة الأصلية المتعمق أحدها. يعمل الفحص الثابت لـ JavaScript و.NET دون محرك لتحليل الشيفرة الأصلية. يستطيع الإعداد تثبيت Hopper بعد الموافقة؛ أما Ghidra وIDA وKuna فتستخدم تثبيتاتك الموجودة. راجع [إعداد الموفّرين](../getting-started/installation.md#hopper).
 
 </details>
 
 <details>
 <summary><strong>هل أحتاج إلى تشغيل Hopper أولًا؟</strong></summary>
 
-يشغّل REA برنامج Hopper عندما تحتاج العملية إليه. على macOS، قد تظهر عند التشغيل الأول نافذة تطلب اختيار وضع العرض التجريبي أو تفعيل الترخيص. راجع [تشغيل Hopper واستكشاف الأخطاء](../installation.md#launcher-paths-and-troubleshooting).
+يشغّل REA برنامج Hopper عندما تحتاج العملية إليه. على macOS، قد تظهر عند التشغيل الأول نافذة تطلب اختيار وضع العرض التجريبي أو تفعيل الترخيص. راجع [تشغيل Hopper واستكشاف الأخطاء](../getting-started/installation.md#launcher-paths-and-troubleshooting).
 
 </details>
 
 <details>
 <summary><strong>ماذا يفعل تثبيت المهارة من skills.sh؟</strong></summary>
 
-توفّر المهارة تعليمات الاستقصاء لوكيلك. استخدم `npx rea-agents setup` لتسجيل خادم MCP الخاص بـ REA وتثبيت التعليمات المطابقة، ثم أعد تشغيل وكيلك. راجع [تثبيت المهارة وحدها](../installation.md#skill-only-installation).
+توفّر المهارة تعليمات الاستقصاء لوكيلك. استخدم `npx rea-agents setup` لتسجيل خادم MCP الخاص بـ REA وتثبيت التعليمات المطابقة، ثم أعد تشغيل وكيلك. راجع [تثبيت المهارة وحدها](../getting-started/installation.md#skill-only-installation).
 
 </details>
 
@@ -342,12 +342,12 @@ npx rea-agents@latest setup
 
 ابدأ بـ [الأدلة العملية](https://rea.tools/ar/guides/) على الموقع. للخيارات الدقيقة والمتطلبات وعقود النتائج:
 
-- [التثبيت والإعداد](../installation.md): تسجيل الوكلاء، وتهيئة الموفّرين، والتحديثات، وإلغاء التثبيت.
-- [الجاهزية واستكشاف الأخطاء](../installation.md#check-readiness-for-your-task): تشخيص وكيل أو محرك تحليل محدد.
-- [CLI وEvidence](../cli.md): الأوامر، واختيار الموفّر، واللقطات، والاستيراد/التصدير، وحالات الخروج.
-- [عقود MCP](../mcp-contracts.md) و[تعليمات الوكلاء](../mcp-prompts.md): نتائج الأدوات، والجلسات، والاستقصاءات الموجّهة.
-- [كتالوج الأدوات](../mcp-contracts.md#generated-catalog): قائمة الأدوات والموفّرين وأوامر CLI المولّدة أثناء البناء.
-- [خطة العمل](../roadmap.md): الأعمال المخطط لها ومتابعة القدرات.
+- [التثبيت والإعداد](../getting-started/installation.md): تسجيل الوكلاء، وتهيئة الموفّرين، والتحديثات، وإلغاء التثبيت.
+- [الجاهزية واستكشاف الأخطاء](../getting-started/installation.md#check-readiness-for-your-task): تشخيص وكيل أو محرك تحليل محدد.
+- [CLI وEvidence](../getting-started/cli.md): الأوامر، واختيار الموفّر، واللقطات، والاستيراد/التصدير، وحالات الخروج.
+- [عقود MCP](../reference/mcp-contracts.md) و[تعليمات الوكلاء](../getting-started/mcp-prompts.md): نتائج الأدوات، والجلسات، والاستقصاءات الموجّهة.
+- [كتالوج الأدوات](../reference/mcp-contracts.md#generated-catalog): قائمة الأدوات والموفّرين وأوامر CLI المولّدة أثناء البناء.
+- [خطة العمل](../development/roadmap.md): الأعمال المخطط لها ومتابعة القدرات.
 
 أبلغ عن الثغرات وفق [SECURITY.md](../../SECURITY.md).
 
@@ -379,7 +379,7 @@ applicable licenses.
 
 نرحّب بمساعدتك في تطوير REA! [افتح issue](https://github.com/morluto/rea/issues) للإبلاغ عن خطأ أو اقتراح ميزة، أو [أرسل pull request](https://github.com/morluto/rea/pulls) لتحسين الشيفرة أو التوثيق.
 
-راجع [CONTRIBUTING.md](../../CONTRIBUTING.md) لإعداد بيئة التطوير والفحوص، و[دليل الاختبار](../testing.md) لمسارات التحقق، و[خريطة البنية](../architecture.mermaid) لهيكل المشروع.
+راجع [CONTRIBUTING.md](../../CONTRIBUTING.md) لإعداد بيئة التطوير والفحوص، و[دليل الاختبار](../development/testing.md) لمسارات التحقق، و[خريطة البنية](../architecture/architecture.mermaid) لهيكل المشروع.
 
 ## الترخيص
 

docs/readme/README_de.md

@@ -10,7 +10,7 @@
 **Eine Funktion gefällt dir? Verstehe, wie sie funktioniert – bis hinunter auf die Binärebene.**
 
 [![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)](../mcp-contracts.md#generated-catalog)
+[![MCP tool catalog](https://img.shields.io/badge/MCP-tool_catalog-5c4ee5?style=flat-square)](../reference/mcp-contracts.md#generated-catalog)
 [![Node.js requirements](https://img.shields.io/badge/Node.js-requirements-339933?style=flat-square&logo=nodedotjs&logoColor=white)](#current-status)
 [![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)
@@ -80,7 +80,7 @@ npx rea-agents setup
 
 Wähle deine Agenten aus, prüfe die geplanten Änderungen und bestätige sie. Die Einrichtung fügt den MCP-Server von REA und passende Workflow-Anweisungen hinzu und sichert vorhandene Konfigurationen. Starte deinen Agenten anschließend neu.
 
-Die Einrichtung unterstützt Claude Code, Codex, Cursor, Gemini CLI, Grok Build und [weitere Agenten](../installation.md#supported-agents). Informationen zur Provider-Konfiguration und manuellen MCP-Registrierung findest du unter [Installation und Einrichtung](../installation.md).
+Die Einrichtung unterstützt Claude Code, Codex, Cursor, Gemini CLI, Grok Build und [weitere Agenten](../getting-started/installation.md#supported-agents). Informationen zur Provider-Konfiguration und manuellen MCP-Registrierung findest du unter [Installation und Einrichtung](../getting-started/installation.md).
 
 MCP verwendet standardmäßig kompakte Eingabeschemas. Für vollständige Feldhinweise und Details zur verschachtelten Validierung setze `REA_MCP_INPUT_SCHEMA_PROFILE=full` in der MCP-Registrierung. Beide Profile behalten alle Tools und dieselbe kanonische Servervalidierung; siehe MCP-Vertragsleitfaden.
 
@@ -109,7 +109,7 @@ npm install --global rea-agents
 rea --help
 ```
 
-Konfiguriere für native Analysen zuerst einen Provider. Native Befehle, Provider-Auswahl, Snapshots und Skriptnutzung beschreibt der [CLI- und Evidence-Leitfaden](../cli.md).
+Konfiguriere für native Analysen zuerst einen Provider. Native Befehle, Provider-Auswahl, Snapshots und Skriptnutzung beschreibt der [CLI- und Evidence-Leitfaden](../getting-started/cli.md).
 
 ### REA aktualisieren
 
@@ -151,45 +151,45 @@ Dein Agent ruft REA über MCP auf, um das Ziel zu untersuchen und relevanten Cod
 
 REA benötigt Node.js 22.x (>=22.23.4), 24.x (>=24.22.1) oder 26+ (>=26.12.1) sowie npm. Zusätzliche Werkzeuge und unterstützte Hostsysteme hängen vom Ziel ab:
 
-| Ziel                                | Was REA zurückgibt                                                                                              | Voraussetzungen und Anleitung                                                                                                                                        |
-| ----------------------------------- | --------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| Native Binärdateien                 | Pseudocode, Assemblercode, Zeichenketten, Symbole, Aufrufe und Verweise                                         | Hopper, Ghidra, IDA oder Kuna; [native Analyse](../native-investigation.md)                                                                                          |
-| Offline-ELF-Struktur                | Sektionen, Segmente, ursprüngliche Symbole/Relokationen und mögliche Schutzmaßnahmen aus statischer Analyse     | Vom Aufrufer bereitgestelltes pwntools unter Linux x64; [Binärdiagnostik](../binary-diagnostics.md)                                                                  |
-| PE certificates                     | Authenticode WIN_CERTIFICATE entries and PKCS#7 signer/X.509 identity fields                                    | Built-in static PE inspection; [PE certificates](../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](../pe-imports.md)                                                                                                        |
-| EVM-Bytecode                        | Dispatch-Selektoren, Byte-Offsets, abgeleitete Argumente und Veränderbarkeit des Zustands                       | Lokale Eingabe mit Rohbytes oder Hexdarstellung unter Linux x64; [Offline-EVM-Leitfaden](../evm-bytecode.md)                                                         |
-| Rust binaries                       | Embedded cargo-auditable dependency list                                                                        | [Rust binaries](../rust-binaries.md)                                                                                                                                 |
-| ELF notes                           | PT_NOTE/SHT_NOTE owners, types, GNU build-id and ABI-tag fields                                                 | Built-in static ELF inspection; [ELF notes](../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](../binary-hardening.md)                                                                                        |
-| Linux kernel modules                | .modinfo keys, __versions CRCs, this_module presence, and signature trailer                                     | Built-in static ELF inspection; [kernel modules](../kernel-modules.md)                                                                                               |
-| Erlang BEAM                         | IFF chunks, atoms, exports, and tables                                                                          | Built-in static BEAM inspection; [Erlang BEAM](../erlang-beam.md)                                                                                                    |
-| Apple IPS crashes                   | .ips metadata, threads, images, registers and crash classes                                                     | Built-in static JSON inspection; [Apple IPS](../apple-ips.md)                                                                                                        |
-| Aufgezeichnete Linux-Abstürze       | Unverarbeitete Note-Einträge, Register/Signale aller aufgezeichneten Threads und optionale Zuordnungskandidaten | Vom Aufrufer bereitgestelltes pwntools unter Linux x64; optional GDB/pwndbg; [aufgezeichnete Abstürze](../recorded-crashes.md)                                       |
-| Desktop-Installationen              | Laufzeitkandidaten, Quelldateien, Komponenten und nächste Schritte                                              | Begrenzte Verzeichnis- und Headerprüfung；[Desktop-Anwendungen](../desktop-applications.md)                                                                          |
-| JavaScript / Electron               | Module, Imports, Source Maps, Routen, IPC und Beziehungen zu nativen Add-ons                                    | Node.js und npm; [Anwendungsanalyse](../javascript-application-workflows.md); Linux: procps `ps`                                                                     |
-| Websites                            | Seitenstruktur, Skripte, Netzwerkbeobachtungen und angeforderte Screenshots                                     | Ein Browser aus der Chrome-Familie; [Browseranalyse](../browser-observation.md)                                                                                      |
-| Gespeicherte Netzwerkaufzeichnungen | Anfragen, Antworten, zugängliche Nutzdaten und Quellpositionen                                                  | HAR / Fiddler Everywhere SAZ; mitmdump unter Linux für Aufzeichnungen im nativen mitmproxy-Format; [Leitfaden zu Netzwerkaufzeichnungen](../web-network-captures.md) |
-| Paketerfassungen                    | Endpunkte, DNS, TLS SNI, Protokollverteilung und HTTP-Anfragen                                                  | Vom Aufrufer bereitgestellte tshark- und capinfos-Binaries; [pcap-Leitfaden](../pcap-analysis.md)                                                                    |
-| .NET-Assemblies                     | Metadaten, CIL-Anweisungen, deklarierte native Abhängigkeiten und Build-Vergleiche                              | Statische Untersuchung; [Leitfaden für verwalteten Code](../managed-code-analysis.md)                                                                                |
-| PyInstaller                         | CArchive, PYZ, Python bytecode                                                                                  | Static inspection; [Python packaged applications](../python-packaged-applications.md)                                                                                |
-| Android-APKs                        | Manifest-Deklarationen, Klassen, dekompilierte Methoden und Verweise                                            | JADX ohne grafische Oberfläche und ein vollständiges JDK unter Linux/macOS/Windows x64; [Android-Leitfaden](../android-analysis.md)                                  |
-| Android-Geräte                      | Geräte, Pakete, Prozesse, Logs, Dumps, Bildschirmaufnahmen sowie APK- und Dateiübertragungen                    | Vom Aufrufer bereitgestelltes adb (Emulator oder Gerät); [ADB-Leitfaden](../adb-device-analysis.md)                                                                  |
-| JEB-Projekte                        | Engine-gestützte Projekteinheiten, Artefakt-Prüfsummen und Pseudokode von Typen/Methoden                        | Ein vom Aufrufer gestarteter JEB-Client mit MCP, ausgewählt über REA_JEB_MCP_URL; [JEB-Leitfaden](../jeb-analysis.md)                                                |
-| Android-Ressourcen                  | Dekodiertes Manifest, String-Tabellen, Sprachen und Versionsfakten                                              | Vom Aufrufer bereitgestellter Apktool-Starter; [Ressourcen-Leitfaden](../apktool-resource-analysis.md)                                                               |
-| Flutter-Apps                        | Dart-Snapshot-Hash, Per-ABI-Bibliotheksprüfsummen und Engine-Build-Provenienz                                   | Keine (statische APK-Analyse); [Flutter-Leitfaden](../flutter-analysis.md)                                                                                           |
-| Firmware                            | Bereiche, Extraktionsergebnisse und Übergaben an die native Analyse                                             | Binwalk / Unblob unter Linux; [Firmware-Leitfaden](../firmware-analysis.md)                                                                                          |
-| Aufgezeichnete Pakete               | Ausgewählte Felder, wiederholte Werte, Filter und Decode-as-Regeln                                              | Linux: TShark 4.x + prlimit; [Mitschnitt-Anleitung](../packet-captures.md)                                                                                           |
-| Aufgezeichnete Logiksignale         | Decoder-Anmerkungen, Sample-Bereiche und Diagnosen                                                              | Linux: sigrok-cli 0.7.2 + prlimit; [Signalaufzeichnungen](../signal-recordings.md)                                                                                   |
-| Pakete und Ressourcen               | Dateiinventare, Hashwerte, plists, Aufbau von Apple-Bundles und extrahierte Ressourcen                          | [Artefakt- und JavaScript-Leitfaden](../javascript-artifact-reconstruction.md), [Apple-Anwendungen](../apple-application-analysis.md)                                |
-| Prozessverhalten                    | Terminalausgabe, Interaktionen, Beobachtungen zu Prozessende und Dateisystem sowie Laufvergleiche               | Linux/macOS mit nativer PTY; [Prozessaufzeichnung](../process-capture.md)                                                                                            |
-| Go-Binärdateien                     | Eingebettete Compilerversion, Module, Ersetzungen und Build-Einstellungen                                       | Integrierte statische Prüfung ELF/PE/thin Mach-O; Keine Go-Installation nötig                                                                                        |
-| SQLite-Datenbanken                  | Tabellen, Spalten, Indizes, Views, Trigger und ausgewählte Zeilen gewöhnlicher Tabellen                         | Lokaler Datenbank/WAL-Snapshot; Node.js 24.x >=24.15 oder 26+ mit nativen SQLite-Grenzen                                                                             |
-| GPU-Codeobjekte                     | CUDA/HIP-Ziele, ausgewählte Kernelparameter und Ressourcen, gespeicherter PTX-Text                              | Integrierte statische Prüfung ELF/PE/fatbin/CUBIN/PTX; [GPU](../gpu-code-objects.md)                                                                                 |
-| Modelldateien                       | GGUF-/safetensors-Metadaten, Tensordeklarationen und abgeleitete Summen                                         | Headerprüfung; optionaler Hash der gesamten Datei; [GGUF / safetensors](../model-artifacts.md)                                                                       |
-| IL2CPP-Metadaten                    | Unity global-metadata.dat: Assembly-Images, Typ-/Methodennamen und Indexbereiche                                | Statische Dekodierung der Versionen 24, 27, 29, 31, 39; kein Unity nötig                                                                                             |
-| Godot PCK                           | Archivinventar und Extraktion, originale Header-/Verzeichnisdaten und ausgewählte Inhaltsidentitäten            | Statische Formate 2, 3, 4; kein Godot nötig                                                                                                                          |
-| WASM-Artefakte                      | Validierung, Sektionen, exakte Import-/Export-WAT-Formen und dekodiertes WAT                                    | Vom Aufrufer bereitgestellt WABT 1.0.42; `inspect_wasm_artifact`                                                                                                     |
-| APK-Signaturen                      | v1/v2/v3/v3.1-Signer, Zertifikatfingerabdrücke, Schlüsselrotation und Digest-Selbstkonsistenz                   | Integrierte statische Prüfung; `inspect_apk_signature`                                                                                                               |
+| Ziel                                | Was REA zurückgibt                                                                                              | Voraussetzungen und Anleitung                                                                                                                                                   |
+| ----------------------------------- | --------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| Native Binärdateien                 | Pseudocode, Assemblercode, Zeichenketten, Symbole, Aufrufe und Verweise                                         | Hopper, Ghidra, IDA oder Kuna; [native Analyse](../guides/native/native-investigation.md)                                                                                       |
+| Offline-ELF-Struktur                | Sektionen, Segmente, ursprüngliche Symbole/Relokationen und mögliche Schutzmaßnahmen aus statischer Analyse     | Vom Aufrufer bereitgestelltes pwntools unter Linux x64; [Binärdiagnostik](../guides/native/binary-diagnostics.md)                                                               |
+| PE certificates                     | Authenticode WIN_CERTIFICATE entries and PKCS#7 signer/X.509 identity fields                                    | Built-in static PE inspection; [PE certificates](../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](../pe-imports.md)                                                                                                                   |
+| EVM-Bytecode                        | Dispatch-Selektoren, Byte-Offsets, abgeleitete Argumente und Veränderbarkeit des Zustands                       | Lokale Eingabe mit Rohbytes oder Hexdarstellung unter Linux x64; [Offline-EVM-Leitfaden](../guides/evm/evm-bytecode.md)                                                         |
+| Rust binaries                       | Embedded cargo-auditable dependency list                                                                        | [Rust binaries](../rust-binaries.md)                                                                                                                                            |
+| ELF notes                           | PT_NOTE/SHT_NOTE owners, types, GNU build-id and ABI-tag fields                                                 | Built-in static ELF inspection; [ELF notes](../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](../binary-hardening.md)                                                                                                   |
+| Linux kernel modules                | .modinfo keys, __versions CRCs, this_module presence, and signature trailer                                     | Built-in static ELF inspection; [kernel modules](../kernel-modules.md)                                                                                                          |
+| Erlang BEAM                         | IFF chunks, atoms, exports, and tables                                                                          | Built-in static BEAM inspection; [Erlang BEAM](../erlang-beam.md)                                                                                                               |
+| Apple IPS crashes                   | .ips metadata, threads, images, registers and crash classes                                                     | Built-in static JSON inspection; [Apple IPS](../apple-ips.md)                                                                                                                   |
+| Aufgezeichnete Linux-Abstürze       | Unverarbeitete Note-Einträge, Register/Signale aller aufgezeichneten Threads und optionale Zuordnungskandidaten | Vom Aufrufer bereitgestelltes pwntools unter Linux x64; optional GDB/pwndbg; [aufgezeichnete Abstürze](../guides/native/recorded-crashes.md)                                    |
+| Desktop-Installationen              | Laufzeitkandidaten, Quelldateien, Komponenten und nächste Schritte                                              | Begrenzte Verzeichnis- und Headerprüfung；[Desktop-Anwendungen](../desktop-applications.md)                                                                                     |
+| JavaScript / Electron               | Module, Imports, Source Maps, Routen, IPC und Beziehungen zu nativen Add-ons                                    | Node.js und npm; [Anwendungsanalyse](../guides/javascript/javascript-application-workflows.md); Linux: procps `ps`                                                              |
+| Websites                            | Seitenstruktur, Skripte, Netzwerkbeobachtungen und angeforderte Screenshots                                     | Ein Browser aus der Chrome-Familie; [Browseranalyse](../guides/web/browser-observation.md)                                                                                      |
+| Gespeicherte Netzwerkaufzeichnungen | Anfragen, Antworten, zugängliche Nutzdaten und Quellpositionen                                                  | HAR / Fiddler Everywhere SAZ; mitmdump unter Linux für Aufzeichnungen im nativen mitmproxy-Format; [Leitfaden zu Netzwerkaufzeichnungen](../guides/web/web-network-captures.md) |
+| Paketerfassungen                    | Endpunkte, DNS, TLS SNI, Protokollverteilung und HTTP-Anfragen                                                  | Vom Aufrufer bereitgestellte tshark- und capinfos-Binaries; [pcap-Leitfaden](../guides/data/pcap-analysis.md)                                                                   |
+| .NET-Assemblies                     | Metadaten, CIL-Anweisungen, deklarierte native Abhängigkeiten und Build-Vergleiche                              | Statische Untersuchung; [Leitfaden für verwalteten Code](../guides/managed/managed-code-analysis.md)                                                                            |
+| PyInstaller                         | CArchive, PYZ, Python bytecode                                                                                  | Static inspection; [Python packaged applications](../python-packaged-applications.md)                                                                                           |
+| Android-APKs                        | Manifest-Deklarationen, Klassen, dekompilierte Methoden und Verweise                                            | JADX ohne grafische Oberfläche und ein vollständiges JDK unter Linux/macOS/Windows x64; [Android-Leitfaden](../guides/android/android-analysis.md)                              |
+| Android-Geräte                      | Geräte, Pakete, Prozesse, Logs, Dumps, Bildschirmaufnahmen sowie APK- und Dateiübertragungen                    | Vom Aufrufer bereitgestelltes adb (Emulator oder Gerät); [ADB-Leitfaden](../guides/android/adb-device-analysis.md)                                                              |
+| JEB-Projekte                        | Engine-gestützte Projekteinheiten, Artefakt-Prüfsummen und Pseudokode von Typen/Methoden                        | Ein vom Aufrufer gestarteter JEB-Client mit MCP, ausgewählt über REA_JEB_MCP_URL; [JEB-Leitfaden](../providers/jeb-analysis.md)                                                 |
+| Android-Ressourcen                  | Dekodiertes Manifest, String-Tabellen, Sprachen und Versionsfakten                                              | Vom Aufrufer bereitgestellter Apktool-Starter; [Ressourcen-Leitfaden](../guides/android/apktool-resource-analysis.md)                                                           |
+| Flutter-Apps                        | Dart-Snapshot-Hash, Per-ABI-Bibliotheksprüfsummen und Engine-Build-Provenienz                                   | Keine (statische APK-Analyse); [Flutter-Leitfaden](../guides/android/flutter-analysis.md)                                                                                       |
+| Firmware                            | Bereiche, Extraktionsergebnisse und Übergaben an die native Analyse                                             | Binwalk / Unblob unter Linux; [Firmware-Leitfaden](../guides/firmware/firmware-analysis.md)                                                                                     |
+| Aufgezeichnete Pakete               | Ausgewählte Felder, wiederholte Werte, Filter und Decode-as-Regeln                                              | Linux: TShark 4.x + prlimit; [Mitschnitt-Anleitung](../guides/data/packet-captures.md)                                                                                          |
+| Aufgezeichnete Logiksignale         | Decoder-Anmerkungen, Sample-Bereiche und Diagnosen                                                              | Linux: sigrok-cli 0.7.2 + prlimit; [Signalaufzeichnungen](../guides/signals/signal-recordings.md)                                                                               |
+| Pakete und Ressourcen               | Dateiinventare, Hashwerte, plists, Aufbau von Apple-Bundles und extrahierte Ressourcen                          | [Artefakt- und JavaScript-Leitfaden](../guides/javascript/javascript-artifact-reconstruction.md), [Apple-Anwendungen](../guides/apple/apple-application-analysis.md)            |
+| Prozessverhalten                    | Terminalausgabe, Interaktionen, Beobachtungen zu Prozessende und Dateisystem sowie Laufvergleiche               | Linux/macOS mit nativer PTY; [Prozessaufzeichnung](../guides/runtime/process-capture.md)                                                                                        |
+| Go-Binärdateien                     | Eingebettete Compilerversion, Module, Ersetzungen und Build-Einstellungen                                       | Integrierte statische Prüfung ELF/PE/thin Mach-O; Keine Go-Installation nötig                                                                                                   |
+| SQLite-Datenbanken                  | Tabellen, Spalten, Indizes, Views, Trigger und ausgewählte Zeilen gewöhnlicher Tabellen                         | Lokaler Datenbank/WAL-Snapshot; Node.js 24.x >=24.15 oder 26+ mit nativen SQLite-Grenzen                                                                                        |
+| GPU-Codeobjekte                     | CUDA/HIP-Ziele, ausgewählte Kernelparameter und Ressourcen, gespeicherter PTX-Text                              | Integrierte statische Prüfung ELF/PE/fatbin/CUBIN/PTX; [GPU](../gpu-code-objects.md)                                                                                            |
+| Modelldateien                       | GGUF-/safetensors-Metadaten, Tensordeklarationen und abgeleitete Summen                                         | Headerprüfung; optionaler Hash der gesamten Datei; [GGUF / safetensors](../model-artifacts.md)                                                                                  |
+| IL2CPP-Metadaten                    | Unity global-metadata.dat: Assembly-Images, Typ-/Methodennamen und Indexbereiche                                | Statische Dekodierung der Versionen 24, 27, 29, 31, 39; kein Unity nötig                                                                                                        |
+| Godot PCK                           | Archivinventar und Extraktion, originale Header-/Verzeichnisdaten und ausgewählte Inhaltsidentitäten            | Statische Formate 2, 3, 4; kein Godot nötig                                                                                                                                     |
+| WASM-Artefakte                      | Validierung, Sektionen, exakte Import-/Export-WAT-Formen und dekodiertes WAT                                    | Vom Aufrufer bereitgestellt WABT 1.0.42; `inspect_wasm_artifact`                                                                                                                |
+| APK-Signaturen                      | v1/v2/v3/v3.1-Signer, Zertifikatfingerabdrücke, Schlüsselrotation und Digest-Selbstkonsistenz                   | Integrierte statische Prüfung; `inspect_apk_signature`                                                                                                                          |
 
 Statische JavaScript- und .NET-Untersuchungen lesen die bereitgestellten Dateien, ohne die Anwendung auszuführen. Laufzeitaufzeichnungen führen das gewählte Ziel mit deinen Benutzerrechten aus oder interagieren damit; die jeweiligen Anleitungen beschreiben die Auswirkungen.
 
@@ -199,7 +199,7 @@ Für die Offline-Untersuchung nativer Binärdateien unterstützt REA auch GNU ob
 
 Bei großen Binärdateien kannst du die Startfrist mit `REA_GHIDRA_STARTUP_TIMEOUT_MS` oder `REA_HOPPER_STARTUP_TIMEOUT_MS` erhöhen.
 
-Native Formate und unterstützte Hostsysteme unterscheiden sich je nach Provider. Siehe [Hopper- und Ghidra-Einrichtung](../installation.md#hopper), den [IDA-Leitfaden](../ida-provider.md), [Kuna](../kuna-provider.md) und die [experimentelle Ghidra-Unterstützung unter Windows](../windows-ghidra-p0.md). Ghidra unterstützt auch [16-Bit-DOS-Analyse](../ghidra-dos.md). Die Provider-Auswahl beschreibt der [CLI-Leitfaden](../cli.md#choose-a-provider). Prüfe die [Verfügbarkeit in Releases](../installation.md#released-package-and-main) für Funktionen, die seit der neuesten npm-Version hinzugekommen sind.
+Native Formate und unterstützte Hostsysteme unterscheiden sich je nach Provider. Siehe [Hopper- und Ghidra-Einrichtung](../getting-started/installation.md#hopper), den [IDA-Leitfaden](../providers/ida-provider.md), [Kuna](../kuna-provider.md) und die [experimentelle Ghidra-Unterstützung unter Windows](../providers/windows-ghidra-p0.md). Ghidra unterstützt auch [16-Bit-DOS-Analyse](../providers/ghidra-dos.md). Die Provider-Auswahl beschreibt der [CLI-Leitfaden](../getting-started/cli.md#choose-a-provider). Prüfe die [Verfügbarkeit in Releases](../getting-started/installation.md#released-package-and-main) für Funktionen, die seit der neuesten npm-Version hinzugekommen sind.
 
 ## Fallstudien
 
@@ -278,28 +278,28 @@ REA exportiert eine lauffähige Umgebung mit einem einfachen Test, der prüft, o
 <details>
 <summary><strong>Welche Agenten können REA verwenden?</strong></summary>
 
-Jeder Agent, der lokale MCP-Server unterstützt. Die Einrichtung konfiguriert die [unterstützten Agenten](../installation.md#supported-agents); andere Clients können die [manuelle MCP-Registrierung](../installation.md#mcp-registry) nutzen.
+Jeder Agent, der lokale MCP-Server unterstützt. Die Einrichtung konfiguriert die [unterstützten Agenten](../getting-started/installation.md#supported-agents); andere Clients können die [manuelle MCP-Registrierung](../getting-started/installation.md#mcp-registry) nutzen.
 
 </details>
 
 <details>
 <summary><strong>Brauche ich Hopper, Ghidra, IDA oder Kuna?</strong></summary>
 
-Für tiefgehende native Analysen wird eines dieser Programme verwendet. Statische JavaScript- und .NET-Untersuchungen funktionieren ohne native Analyse-Engine. Die Einrichtung kann Hopper nach Zustimmung installieren; Ghidra, IDA und Kuna nutzen deine vorhandenen Installationen. Siehe [Provider-Einrichtung](../installation.md#hopper).
+Für tiefgehende native Analysen wird eines dieser Programme verwendet. Statische JavaScript- und .NET-Untersuchungen funktionieren ohne native Analyse-Engine. Die Einrichtung kann Hopper nach Zustimmung installieren; Ghidra, IDA und Kuna nutzen deine vorhandenen Installationen. Siehe [Provider-Einrichtung](../getting-started/installation.md#hopper).
 
 </details>
 
 <details>
 <summary><strong>Muss ich Hopper vorher starten?</strong></summary>
 
-REA startet Hopper, wenn eine Operation es benötigt. Unter macOS kann beim ersten Start ein Dialog erscheinen, in dem du den Demomodus auswählst oder deine Lizenz aktivierst. Siehe [Hopper-Start und Fehlerbehebung](../installation.md#launcher-paths-and-troubleshooting).
+REA startet Hopper, wenn eine Operation es benötigt. Unter macOS kann beim ersten Start ein Dialog erscheinen, in dem du den Demomodus auswählst oder deine Lizenz aktivierst. Siehe [Hopper-Start und Fehlerbehebung](../getting-started/installation.md#launcher-paths-and-troubleshooting).
 
 </details>
 
 <details>
 <summary><strong>Was bewirkt die Installation des Skills über skills.sh?</strong></summary>
 
-Der Skill stellt Untersuchungsanweisungen für deinen Agenten bereit. Verwende `npx rea-agents setup`, um den MCP-Server von REA zu registrieren und passende Anweisungen zu installieren. Starte deinen Agenten anschließend neu. Siehe [Installation nur des Skills](../installation.md#skill-only-installation).
+Der Skill stellt Untersuchungsanweisungen für deinen Agenten bereit. Verwende `npx rea-agents setup`, um den MCP-Server von REA zu registrieren und passende Anweisungen zu installieren. Starte deinen Agenten anschließend neu. Siehe [Installation nur des Skills](../getting-started/installation.md#skill-only-installation).
 
 </details>
 
@@ -342,12 +342,12 @@ Wenn du einen Agenten verwendest, schließe die [Aktualisierung der Einrichtung]
 
 Beginne mit den [praxisnahen Anleitungen](https://rea.tools/de/guides/) auf der Website. Genaue Optionen, Voraussetzungen und Ergebniskontrakte findest du hier:
 
-- [Installation und Einrichtung](../installation.md): Agentenregistrierung, Provider-Konfiguration, Updates und Deinstallation.
-- [Bereitschaft und Fehlerbehebung](../installation.md#check-readiness-for-your-task): Diagnose eines bestimmten Agenten oder einer Analyse-Engine.
-- [CLI und Evidence](../cli.md): Befehle, Provider-Auswahl, Snapshots, Import/Export und Exit-Status.
-- [MCP-Kontrakte](../mcp-contracts.md) und [Agenten-Prompts](../mcp-prompts.md): Werkzeugergebnisse, Sitzungen und geführte Untersuchungen.
-- [Werkzeugkatalog](../mcp-contracts.md#generated-catalog): Beim Build erzeugtes Inventar von Werkzeugen, Providern und CLI-Befehlen.
-- [Roadmap](../roadmap.md): Geplante Arbeiten und Fortschrittsübersichten zu Fähigkeiten.
+- [Installation und Einrichtung](../getting-started/installation.md): Agentenregistrierung, Provider-Konfiguration, Updates und Deinstallation.
+- [Bereitschaft und Fehlerbehebung](../getting-started/installation.md#check-readiness-for-your-task): Diagnose eines bestimmten Agenten oder einer Analyse-Engine.
+- [CLI und Evidence](../getting-started/cli.md): Befehle, Provider-Auswahl, Snapshots, Import/Export und Exit-Status.
+- [MCP-Kontrakte](../reference/mcp-contracts.md) und [Agenten-Prompts](../getting-started/mcp-prompts.md): Werkzeugergebnisse, Sitzungen und geführte Untersuchungen.
+- [Werkzeugkatalog](../reference/mcp-contracts.md#generated-catalog): Beim Build erzeugtes Inventar von Werkzeugen, Providern und CLI-Befehlen.
+- [Roadmap](../development/roadmap.md): Geplante Arbeiten und Fortschrittsübersichten zu Fähigkeiten.
 
 Melde Sicherheitslücken gemäß [SECURITY.md](../../SECURITY.md).
 
@@ -379,7 +379,7 @@ applicable licenses.
 
 Wir freuen uns über deine Hilfe bei REA! [Öffne ein Issue](https://github.com/morluto/rea/issues), um einen Fehler zu melden oder eine Funktion vorzuschlagen, oder [sende einen Pull Request](https://github.com/morluto/rea/pulls), um Code oder Dokumentation zu verbessern.
 
-Die Entwicklungsumgebung und Prüfungen beschreibt [CONTRIBUTING.md](../../CONTRIBUTING.md), die Verifikationspfade der [Testleitfaden](../testing.md) und die Projektstruktur die [Architekturübersicht](../architecture.mermaid).
+Die Entwicklungsumgebung und Prüfungen beschreibt [CONTRIBUTING.md](../../CONTRIBUTING.md), die Verifikationspfade der [Testleitfaden](../development/testing.md) und die Projektstruktur die [Architekturübersicht](../architecture/architecture.mermaid).
 
 ## Lizenz