chore: combine trace and function evidence prototypes

* fix(ghidra): mark empty xrefs results as unresolved, not unreferenced

Ghidra 12.2 resolves no references to data addresses on some Mach-O
imports, and xrefs returned a bare empty list with nothing separating
'no references exist' from 'this provider resolved no references', so
callers concluded addresses were unreferenced.

projectExecution now attaches ghidraEmptyXrefsLimitation to an empty
xrefs result: the list reflects what this analysis resolved, not proof
the address is unreferenced. Non-empty results carry no caveat.

Covered by behavior tests for both branches; validated against
FM9-Edit-arm64 (expect: limitation) once the daemon session reopens.

* fix(ghidra): drop circular trace_feature cross-check from empty xrefs caveat

trace_feature calls xrefs internally, so recommending it as an independent
cross-check repeats the same lookup the caveat qualifies. Keep disassembly
as the single independent check.

* fix(ghidra): report actionable-reference absence and invalidate stale snapshots

Review follow-up on the empty xrefs caveat:
- The bridge filters synthetic entry-point references before observation, so
  "resolved no references" could be false; the caveat now reports that no
  actionable references were returned and names the omission.
- Drop the trace_feature cross-check: traceReferences observes xrefs per
  matched string, repeating the same lookup instead of independent evidence.
- Bump instruction_references semantics to v3 so analysis snapshots captured
  before the caveat replay no bare empty results; the profile commitment in
  the snapshot binding no longer matches.

* feat(ghidra): mark empty function-reference facets as unresolved too

Extends the empty-xrefs caveat to the sibling ReferenceManager consumers
review follow-up identified: procedure_references and analyze_function
reference facets built on the same observation path could still present
empty arrays as collected facts.

- ghidraEmptyFunctionReferencesLimitation attaches when
  procedure_references returns no references for the requested direction
  and when a dossier observes no references in either direction;
  callers/callees (function-manager derived, observed working on the
  reported target) stay caveat-free.
- One emptyReferenceCaveat owner replaces the inline xrefs branch.
- function_references semantics bump to v3 so snapshots captured before
  the caveat do not replay bare empty facets; raw profile digests
  recomputed.

* fix(ghidra): cover annotation and instruction reference facets in the caveat

Review follow-up: annotate_native_function returns a dossier built by the
same analyzeFunction collection and inspect_native_instruction builds
incoming_references with visitObservedReferencesTo; both could present
empty arrays as collected facts under the reported ReferenceManager
failure.

- annotate_native_function attaches the caveat when its dossier observes
  no references in either direction.
- inspect_native_instruction attaches it when incoming_references is an
  explicit empty array (null or omission stays unavailable, matching the
  field contract).
- Split the diagnostics describe to keep each block under the lint bound.
- Behavior tests cover attach and non-attach for both operations.

* fix(ghidra): name the honest cross-check limits in the reference caveats

Review follow-up: the motivating failure was a string address, so
'cross-check the disassembly at this address' pointed at nothing — data
and string addresses have no instruction to disassemble — and
inspect_native_instruction's incoming_references is built through the
same visitObservedReferencesTo path, so it was not independent either.

- xrefs caveat now states that no independent in-product cross-check
  exists for the empty result, that surrounding disassembly only helps
  at a code address, and that data or string addresses need an external
  disassembly scan (otool -tV adrp/add pairing).
- Function-facet caveat separates outgoing references (own disassembly
  is independent) from incoming references (no in-product check; scan
  other code externally).

* fix(ghidra): use the address-scoped caveat for inspect_native_instruction

Greptile review follow-up: inspect_native_instruction checks incoming
references to one exact address, so the function-scoped caveat misdescribed
the scope; an instruction can be unreferenced while its function has
references elsewhere, and the address may have no containing function.
Attach the address-scoped xrefs caveat instead.

* fix(ghidra): qualify each empty reference direction independently

Analyze-function and annotate-native-function results attached the
unresolved-references caveat only when BOTH reference directions were
empty, so a dossier with one populated direction presented its empty
direction as a collected fact.

Split the combined function-references caveat into direction-scoped
limitations and attach one per empty direction (analyze_function,
annotate_native_function dossier readback, procedure_references by its
requested direction).

* fix(ghidra): qualify empty outgoing instruction references

inspect_native_instruction results carry two independent
ReferenceManager facets: the incoming list and the outgoing references
built from instruction.getReferencesFrom(). Only the incoming list was
checked, so an instruction with a populated incoming list and no
outgoing references presented the empty outgoing facet as a collected
fact, and any populated incoming list suppressed the caveat entirely.

Each facet is now qualified independently: the empty incoming list
keeps the address-scoped caveat; the empty outgoing list attaches the
new instruction-scoped outgoing limitation (this stream is not
entry-point filtered, so it claims no entry-point omission). Truth
table covered in describe("Ghidra empty instruction reference facets").

* fix(ghidra): gate the instruction outgoing caveat on decoded status

Non-decoded inspect_native_instruction results (data, not-in-listing,
not-instruction-boundary, outside-memory) return before the bridge ever
queries instruction.getReferencesFrom(), so their empty references list
is an unobserved facet, not an empty ReferenceManager observation. The
unconditional outgoing caveat claimed the ReferenceManager returned no
references from an instruction that does not exist at that address.

The outgoing limitation now attaches only when status is decoded; the
address-scoped incoming caveat still applies per the empty incoming
list, matching the original motivating data-address case.

* fix(ghidra): dossier incoming omission and external outgoing recovery

Two unqualified cases remained in the function-reference caveats:

- The analyze_function/annotation dossier excludes incoming references
  whose source is inside the function's own body (a self-recursive call
  is enough), so the projected empty list can mean 'no outside source
  observed' or 'only in-body sources observed'. The dossier now uses a
  dedicated incoming limitation naming the exclusion, pointing at the
  outgoing edges/disassembly where in-body edges remain visible, and at
  procedure_references(incoming) - the same ReferenceManager stream
  without the in-body exclusion - as the in-product discriminator.
  procedure_references keeps the generic incoming caveat: its incoming
  stream is not in-body filtered.

- An external function has no local body, so the outgoing caveat's
  'function's own disassembly' recommendation was impossible. Records
  classified external now get an external-specific outgoing limitation
  naming the defining artifact and this program's call sites instead
  (procedure_references outgoing, analyze_function, annotation readback).

* fix(ghidra): qualify dossier incoming caveat observation

The dossier-specific incoming caveat claimed the ReferenceManager
observed no incoming references from outside the body, but
visitObservedReference (ReaGhidraBridge.java:3973-3974) drops
entry-point references before the body filter (1619-1621), so the
manager may have returned references the dossier never reports.
Reframe as 'returned no actionable' and name both omissions; correct
the recovery claim: procedure_references(incoming) lacks the in-body
filter but omits synthetic entry-point references as well.

.github/pull_request_template.md

@@ -106,7 +106,8 @@ limits, security/privacy/containment implications, and meaningful proof gaps. --
 
 ## Author readiness
 
-<!-- The human owner completes these declarations before requesting review.
+<!-- The human owner completes these declarations before requesting review,
+unless the PR author is exempt as listed in CONTRIBUTING.md.
 The PR author is the owner by default. A different owner must explicitly accept
 ownership on this PR.
 AI agents must leave these declarations to a human to dictate to them or there could be catastrophic consequences for many users of REA.

.github/workflows/ci.yml

@@ -807,6 +807,8 @@ jobs:
           tests/boundary/mcp/nativeDemangleMcp.test.ts
           tests/boundary/mcp/nativeMachoSummaryMcp.test.ts
           tests/boundary/providers/native/nativeSignatureTargetBinding.test.ts
+          tests/boundary/providers/native/nativeUiOffscreenWindow.test.ts
+          tests/boundary/process/nativeUiVerifierLane.test.ts
           tests/boundary/cli/nativeSignatureCli.test.ts
           tests/boundary/cli/nativeMachoArm64_32Cli.test.ts
           tests/boundary/cli/nativeMachoEncryptionCli.test.ts

.github/workflows/real-binary-layout.yml

@@ -55,12 +55,12 @@ jobs:
       - uses: ./.github/actions/portable-build-cache
         with:
           build_cache_artifact: ${{ inputs.build_cache_artifact }}
-      - name: Install ELF32 cross toolchains for source-owned fixtures
+      - name: Install AArch64 and ELF32 cross toolchains for source-owned fixtures
         run: |
           sudo apt-get update
           sudo apt-get install --yes --no-install-recommends \
-            gcc-i686-linux-gnu gcc-arm-linux-gnueabi gcc-mips-linux-gnu gcc-mipsel-linux-gnu \
-            libc6-dev-i386-cross libc6-dev-armel-cross libc6-dev-mips-cross libc6-dev-mipsel-cross
+            gcc-aarch64-linux-gnu gcc-i686-linux-gnu gcc-arm-linux-gnueabi gcc-mips-linux-gnu gcc-mipsel-linux-gnu \
+            libc6-dev-arm64-cross libc6-dev-i386-cross libc6-dev-armel-cross libc6-dev-mips-cross libc6-dev-mipsel-cross
       - name: Acquire exact upstream libraries in an isolated runner environment
         shell: bash
         run: |

.github/workflows/website-check.yml

@@ -21,6 +21,10 @@ jobs:
           python-version: "3.12"
           cache: pip
           cache-dependency-path: website/requirements.txt
+      - name: Set up Node.js for the website Worker checks
+        uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4.4.0
+        with:
+          node-version-file: .nvmrc
       - name: Install sharing-image dependencies
         run: |
           sudo apt-get update

.github/workflows/website-pages.yml

@@ -54,6 +54,10 @@ jobs:
           python-version: "3.12"
           cache: pip
           cache-dependency-path: website/requirements.txt
+      - name: Set up Node.js for the website Worker checks
+        uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4.4.0
+        with:
+          node-version-file: .nvmrc
       - name: Install sharing-image dependencies
         run: |
           sudo apt-get update
@@ -75,10 +79,21 @@ jobs:
           PY
       - name: Configure Pages
         uses: actions/configure-pages@983d7736d9b0ae728b81ab479565c72886d7745b # v5.0.0
+      # upload-pages-artifact excludes dot directories, including .well-known.
+      - name: Package the website including agent discovery
+        run: |
+          tar --dereference --hard-dereference --directory website/_site \
+            --exclude=.git --exclude=.github -cf "$RUNNER_TEMP/artifact.tar" .
+          tar -tf "$RUNNER_TEMP/artifact.tar" \
+            ./.well-known/ard.json ./.well-known/ai-catalog.json \
+            ./.well-known/agent-skills/index.json > /dev/null
       - name: Upload the website
-        uses: actions/upload-pages-artifact@7b1f4a764d45c48632c6b24a0339c27f5614fb0b # v4.0.0
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2
         with:
-          path: website/_site
+          name: github-pages
+          path: ${{ runner.temp }}/artifact.tar
+          retention-days: 1
+          if-no-files-found: error
 
   deploy:
     needs: prepare
@@ -130,14 +145,24 @@ jobs:
           PUBLISH_TARGET: ${{ inputs.target }}
         run: |
           python3 -u - <<'PY'
+          import hashlib
           import json
           import os
           import sys
           import time
           from urllib.error import URLError
-          from urllib.parse import urljoin
+          from urllib.parse import urljoin, urlsplit
           from urllib.request import Request, urlopen
 
+          def open_public(url, accept=None):
+              headers = {
+                  "Cache-Control": "no-cache",
+                  "User-Agent": "REA-Website-Verifier/1.0 (+https://github.com/morluto/rea)",
+              }
+              if accept:
+                  headers["Accept"] = accept
+              return urlopen(Request(url, headers=headers), timeout=10)
+
           expected = os.environ["GITHUB_SHA"]
           pages_url = os.environ["PAGES_URL"]
           if not pages_url:
@@ -153,11 +178,7 @@ jobs:
               for name, base in list(pending.items()):
                   url = urljoin(base, "deployment.json") + "?commit=" + expected
                   try:
-                      request = Request(url, headers={
-                          "Cache-Control": "no-cache",
-                          "User-Agent": "REA-Website-Verifier/1.0 (+https://github.com/morluto/rea)",
-                      })
-                      with urlopen(request, timeout=10) as response:
+                      with open_public(url) as response:
                           actual = json.load(response).get("commit")
                       if actual == expected:
                           print(f"{name} serves {expected}: {base}")
@@ -172,6 +193,27 @@ jobs:
                   time.sleep(5)
           if pending:
               sys.exit("Could not verify published revision on: " + ", ".join(pending))
+          for name, base in hosts.items():
+              with open_public(urljoin(base, ".well-known/agent-skills/index.json")) as response:
+                  skill, = json.load(response)["skills"]
+              # Fetch from each selected host, including the /rea/ mirror.
+              artifact_url = urljoin(base, urlsplit(skill["url"]).path.lstrip("/"))
+              with open_public(artifact_url) as response:
+                  digest = "sha256:" + hashlib.sha256(response.read()).hexdigest()
+              if digest != skill["digest"]:
+                  sys.exit(name + " serves a skill archive with the wrong digest")
+              for manifest in ("ard.json", "ai-catalog.json"):
+                  with open_public(urljoin(base, ".well-known/" + manifest)) as response:
+                      if not json.load(response).get("entries"):
+                          sys.exit(name + " serves an empty discovery manifest")
+              if name == "Cloudflare":
+                  with open_public(base, accept="text/markdown") as response:
+                      vary = {value.strip().lower() for value in response.headers.get("Vary", "").split(",")}
+                      if response.headers.get_content_type() != "text/markdown" or "accept" not in vary:
+                          sys.exit("Cloudflare did not negotiate Markdown with Vary: Accept")
+                      if 'rel="ard"' not in response.headers.get("Link", ""):
+                          sys.exit("Cloudflare is missing its discovery Link header")
+              print(name + " serves the discovery manifests and verified skill archive")
           with open(os.environ["GITHUB_STEP_SUMMARY"], "a", encoding="utf-8") as summary:
               links = " and ".join(f"[{name}]({url})" for name, url in hosts.items())
               summary.write(f"Published commit `{expected}` to {links}.\n")

AGENTS.md

@@ -128,8 +128,8 @@ owner to complete. Never attest to human review on their behalf. Draft status
 is optional; preserve the PR's current draft status unless the user asks to change
 it. Later pushes do not invalidate the readiness declaration or require another
 human sign-off. Keep the PR body and affected validation current as work changes.
-The readiness check validates
-the filled declaration; CI and automated review results do not establish that
+The readiness check validates the filled declaration or the author exemption
+listed in CONTRIBUTING.md; CI and automated review results do not establish that
 human review occurred, maintainer scope approval, or merge permission.
 
 <!-- BEGIN:turborepo-agent-rules -->

CONTRIBUTING.md

@@ -93,7 +93,8 @@ Before requesting maintainer review, the human owner must:
   passing. Follow the [verification requirements](#development-feedback-and-pr-verification)
   for required checks and real-provider coverage.
 - Complete the **Author readiness** declaration in the PR template, explicitly
-  stating that the PR is ready for initial review.
+  stating that the PR is ready for initial review, unless the PR author is
+  exempt from the declaration as listed below.
 
 Keep the PR description concise and current. Explain the problem, observable
 outcome, approach, and useful evidence; link long logs or put them in optional
@@ -114,9 +115,12 @@ validation current as work changes. AI agents must leave human declarations to
 the human owner and must not attest to a human review on their behalf.
 
 The `PR readiness` check reports pending for drafts and requires a named human
-owner and all three template declarations for non-drafts. It checks that the
-declaration is filled, not whether the code or evidence is correct. Existing PRs
-can copy the **Author readiness** section from the current template.
+owner and all three template declarations for non-drafts. PRs authored by
+@morluto, @kaoru0822-kitauji, @N0zoM1z0, or @gensokyo-dev are exempt from
+the declaration; their human ownership, review, and evidence responsibilities
+above still apply. The check identifies authors by GitHub account ID. It checks
+that the declaration is filled, not whether the code or evidence is correct.
+Existing PRs can copy the **Author readiness** section from the current template.
 Open PRs must have distinct head commits because GitHub shares commit statuses.
 
 Maintainers enable merge enforcement after the workflow is merged: run

README.md

@@ -20,6 +20,8 @@
 
 **[Website](https://rea.tools/) · [Guides](https://rea.tools/guides/) · [Showcases](https://rea.tools/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="Join the REA community on Discord" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [Quick start](#quick-start) · [How REA works](#how-rea-works) · [What you can analyze](#what-you-can-analyze) · [Showcases](#showcases) · [Build RL environments](#build-rl-environments) · [FAQ](#faq) · [Documentation](#documentation)
 
 <code>npx rea-agents setup</code>

THIRD_PARTY_NOTICES.md

@@ -60,7 +60,7 @@ pin inspection sources; they are not included in the npm package.
 | 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/v1.988/LICENSE), with its [NOTICE](https://github.com/Noelo-Lab/kuna/blob/v1.988/NOTICE)                                                                                                             | Bring your own `kuna`; REA verified 1.988 and never downloads, installs or bundles it. REA invokes it as a separate process.                                                                                                                                                       |
+| 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.                                                                                                                                                                                                                        |

bridge/native/ReaNativeUI.swift

@@ -65,7 +65,10 @@ func observe(_ request: Request) async throws -> [String: Any] {
   guard SHA256.hash(data: executableBytes).map({ String(format: "%02x", $0) }).joined() == request.sha256 else {
     try fail("target-mismatch", "Running executable bytes differ from the active target digest")
   }
-  guard let windows = CGWindowListCopyWindowInfo([.optionIncludingWindow], request.window_id) as? [[String: Any]],
+  // .optionIncludingWindow omits a selected window while it is off screen, which
+  // is not absence: select from every window, and let capture report what it can.
+  guard let windows = (CGWindowListCopyWindowInfo([.optionAll], kCGNullWindowID) as? [[String: Any]])?
+    .filter({ ($0[kCGWindowNumber as String] as? NSNumber)?.uint32Value == request.window_id }),
     windows.count == 1, let window = windows.first,
     (window[kCGWindowOwnerPID as String] as? NSNumber)?.int32Value == request.pid,
     (window[kCGWindowLayer as String] as? NSNumber)?.intValue == 0,

bridge/process/ProcessRunTokenReader.swift

@@ -228,6 +228,22 @@ func processRunTokenObservation(
   parse: Result<ParsedRunToken, RunTokenReadError>,
   codeSigningFlags: () -> UInt32?
 ) -> RunTokenObservation {
+  // Native inspection restrictions apply even when argv is incomplete or
+  // overwritten, before parsing reaches the environment. Keep this fact at
+  // the native boundary; cleanup still decides whether the process is related.
+  func withheldEnvironment() -> RunTokenObservation? {
+    guard let flags = codeSigningFlags() else { return nil }
+    if (flags & csPlatformBinary) != 0 {
+      return unavailable(pid: pid, reason: "platform_binary_environment_withheld")
+    }
+    if (flags & csRestrict) != 0 {
+      return unavailable(pid: pid, reason: "restricted_process_environment_withheld")
+    }
+    return nil
+  }
+  func unavailableEnvironment(_ reason: String) -> RunTokenObservation {
+    withheldEnvironment() ?? unavailable(pid: pid, reason: reason)
+  }
   switch parse {
   case .success(let parsed):
     if let runId = parsed.runId {
@@ -238,40 +254,25 @@ func processRunTokenObservation(
     if parsed.environmentEntryCount > 0 {
       return RunTokenObservation(pid: pid, state: "readable", run_id: nil, reason: nil)
     }
-    let flags = codeSigningFlags()
-    if let flags, (flags & csPlatformBinary) != 0 {
-      return unavailable(pid: pid, reason: "platform_binary_environment_withheld")
-    }
-    if let flags, (flags & csRestrict) != 0 {
-      return unavailable(pid: pid, reason: "restricted_process_environment_withheld")
-    }
+    if let withheld = withheldEnvironment() { return withheld }
     return RunTokenObservation(pid: pid, state: "readable", run_id: nil, reason: nil)
   case .failure(let failure):
     switch failure {
     case .environmentUnavailable:
-      let flags = codeSigningFlags()
-      if let flags, (flags & csPlatformBinary) != 0 {
-        return unavailable(pid: pid, reason: "platform_binary_environment_withheld")
-      }
-      if let flags, (flags & csRestrict) != 0 {
-        return unavailable(pid: pid, reason: "restricted_process_environment_withheld")
-      }
-      return unavailable(pid: pid, reason: "environment_unavailable")
+      return unavailableEnvironment("environment_unavailable")
     case .ambiguousEnvironmentBoundary:
-      if let flags = codeSigningFlags(), (flags & csRestrict) != 0 {
-        return unavailable(pid: pid, reason: "restricted_process_environment_withheld")
-      }
-      return unavailable(pid: pid, reason: "ambiguous_environment_boundary")
+      return unavailableEnvironment("ambiguous_environment_boundary")
+    // These failures already establish that token bytes were available.
     case .duplicateToken:
       return unavailable(pid: pid, reason: "duplicate_run_token")
     case .invalidTokenEncoding:
       return unavailable(pid: pid, reason: "invalid_run_token_encoding")
     case .appleVectorUnavailable:
-      return unavailable(pid: pid, reason: "apple_vector_unavailable")
+      return unavailableEnvironment("apple_vector_unavailable")
     case .invalidBuffer:
-      return unavailable(pid: pid, reason: "malformed_procargs")
+      return unavailableEnvironment("malformed_procargs")
     case .invalidBufferAt(let stage):
-      return unavailable(pid: pid, reason: "malformed_procargs_\(stage.rawValue)")
+      return unavailableEnvironment("malformed_procargs_\(stage.rawValue)")
     }
   }
 }

bridge/pwntools/layout_impl.py

@@ -16,10 +16,10 @@ PROFILE = "[email protected];[email protected];[email protected]"
 PACKAGES = {"pwntools": "4.15.0", "pyelftools": "0.33", "unicorn": "2.1.2"}
 OUTPUT_BYTES = 64 * 1024 * 1024
 # (e_machine, ELF class bits, byte order) -> architecture pwntools must also report.
-PROFILES = {(62, 64, "little"): "amd64", (3, 32, "little"): "i386", (40, 32, "little"): "arm",
-            (8, 32, "little"): "mips", (8, 32, "big"): "mips"}
-PROFILE_SCOPE = ("Layout profile requires ELF64 x86-64, ELF32 i386, ELF32 ARM little-endian "
-                 "or ELF32 MIPS little- or big-endian objects.")
+PROFILES = {(62, 64, "little"): "amd64", (183, 64, "little"): "aarch64", (3, 32, "little"): "i386",
+            (40, 32, "little"): "arm", (8, 32, "little"): "mips", (8, 32, "big"): "mips"}
+PROFILE_SCOPE = ("Layout profile requires ELF64 x86-64, ELF64 AArch64 little-endian, ELF32 i386, "
+                 "ELF32 ARM little-endian or ELF32 MIPS little- or big-endian objects.")
 
 
 class LayoutFailure(Exception):

docs/agent-environments.md

@@ -1149,7 +1149,12 @@ global conflict involving an equal pair is not used to normalize either pair; th
 
 A step agrees when the statuses and the normalised bodies are equal. The report gives agreement overall, per probe and
 per tool, `agreement_ignoring_order` for steps that differ only in item order, and each step's differences, at most 20,
-with a JSON pointer and both values cut short:
+with a JSON pointer and both values cut short. Each step reports `differences_total` before that cap,
+`differences_omitted`, and `differences_truncated` (true when entries were omitted). Agreement and categories use the
+complete comparison. Omitted entries are not retained, so `--full-output` cannot recover them; inspect the original
+capture and probe Evidence to investigate beyond the returned pointers.
+
+The difference categories are:
 
 | Category        | Meaning                                                                                                      |
 | --------------- | ------------------------------------------------------------------------------------------------------------ |

docs/binary-diagnostics.md

@@ -9,9 +9,11 @@ ordinary binary inspection use the same modular capability.
 ## Bring your own engine
 
 Real verification covers **Linux x64** hosts and **EXEC/DYN/REL** objects in
-these profiles: ELF64 x86-64, ELF32 i386, ELF32 little-endian ARM and ELF32
-little- or big-endian MIPS. Other machines, classes and byte orders, including
-AArch64 and big-endian ARM, return `unsupported_target`. Provide an absolute
+these profiles: ELF64 x86-64, ELF64 little-endian AArch64, ELF32 i386, ELF32
+little-endian ARM and ELF32 little- or big-endian MIPS. Other machines, classes
+and byte orders, including big-endian ARM, return `unsupported_target`. Other
+hosts, including Linux arm64, return `capability_unavailable` naming the
+detected host before any target is read. Provide an absolute
 Python executable whose environment already contains unchanged pwntools 4.15.0,
 pyelftools 0.33 and Unicorn 2.1.2:
 

docs/browser-observation.md

@@ -500,7 +500,7 @@ REA retains local observation data and removes only URL userinfo credentials, ex
   connection/frame inventories; matching direction/opcode sequences alone do
   not prove alignment after drops. Redirect resource types use only shared known metadata:
   an omitted type leaves equality unknown rather than proving a modification.
-- Console observations with a stack source retain call type, argument types, the CDP `Runtime.Timestamp` in milliseconds since Unix epoch, and source location. An absent or invalid timestamp is `null` and makes `console_events` incomplete; an observed zero remains zero. Argument types are listed by CDP argument position. An absent or non-array argument inventory is `null`, and a malformed argument keeps its position as `unknown`; either makes `console_events` incomplete, while an observed empty inventory remains `[]`. A malformed stack or top stack frame is not replaced by its caller: the console event is excluded, and a request initiator location or WebMCP `registration_source` is `null`; each is reported as `invalid_protocol_value`. This epoch-millisecond clock is separate from the monotonic-second timestamps in `observe-web-session`. When console text capture is selected, already-delivered primitive values are retained verbatim with their original `argument_index`; objects, getters, and remote properties are never expanded. Text capture is `unavailable` when the argument inventory is unknown.
+- Console observations with a stack source retain call type, argument types, the CDP `Runtime.Timestamp` in milliseconds since Unix epoch, and source location. An absent or invalid timestamp is `null` and makes `console_events` incomplete; an observed zero remains zero. Argument types are listed by CDP argument position. An absent or non-array argument inventory is `null`, and a malformed argument keeps its position as `unknown`; either makes `console_events` incomplete, while an observed empty inventory remains `[]`. A malformed stack or top stack frame is not replaced by its caller: the console event is excluded, and a request initiator location or WebMCP `registration_source` is `null`; each is reported as `invalid_protocol_value`. Source locations are CDP's zero-based lines and UTF-16 columns. A negative column, which Chrome reports on the first line of some inline scripts, is kept as reported and does not locate a column in the source URL; an invalid line or a non-integer column is `null` (WebMCP `registration_source` is `null`) and is reported as `invalid_protocol_value`. This epoch-millisecond clock is separate from the monotonic-second timestamps in `observe-web-session`. When console text capture is selected, already-delivered primitive values are retained verbatim with their original `argument_index`; objects, getters, and remote properties are never expanded. Text capture is `unavailable` when the argument inventory is unknown.
 - WebSocket observations retain direction, opcode, and payload byte length. A missing or malformed CDP opcode is returned as `null`, with opcode-dependent payload byte length and shape also `null`, and marks `websocket_frames` incomplete. Missing or wrong-typed payload data is not treated as empty; its byte length is `null`, and a text payload shape is unknown. Numeric opcode `0` and an observed empty payload remain distinct from missing data. Opcode is nullable in the public inspection schema, so clients must handle unknown protocol values. When shape capture is selected, text messages are classified as text or complete value-free JSON shape; binary bytes, hashes, prefixes, and raw payloads are never retained.
 - Storage observations always redact values. Key names, IndexedDB names, and cache names require `include_storage_keys`; stable content fingerprints require the additional `include_storage_fingerprints` selection. Cookie fingerprints cover cookies applicable to the current main-frame URL, including its path, rather than every cookie path on that origin. Other storage remains scoped to the origin. Cache fingerprints hash all decoded response bytes, including bodies above 64 KiB, subject to the [64 MiB per-message CDP limit](#request-boundary). Missing or undecodable cache bodies and partial IndexedDB remote objects make fingerprint coverage incomplete, so identical observations remain `unknown`.
 - Unavailable or malformed storage inventories mark `storage_keys` unavailable, even without fingerprints. Comparisons suppress inferred key additions and removals while preserving modifications proven by complete fingerprints on both sides. Previously exported captures are not retroactively corrected; recapture them to obtain these coverage markers.

docs/cli.md

@@ -569,6 +569,17 @@ prints a failure, so it omits the same-session reuse and
 `parameter`) for a new invocation and rerun. For example, a Ghidra decompile
 deadline names `REA_GHIDRA_DECOMPILE_TIMEOUT_SECONDS`.
 
+`rea debug-with-gdb` and `rea debug-with-rizin` hold their debugger only for the
+command's own process. If cleanup cannot confirm the debugger stopped, they print
+`cleanup_incomplete` and exit nonzero without stopping it. `remediation.action`
+names the process, as does `retained_debugger_pids` in `details.diagnostics`, or
+in `details.diagnostics.cleanup_error.details.diagnostics` when the command also
+failed or was interrupted. Exiting closes the debugger's command and output pipes.
+REA does not establish what the debugger or its target does next, so check that
+process. An MCP server that shuts down likewise exits with status 1 instead of
+waiting on a debugger it could not stop. It names the process on stderr and as
+`retained_debugger_pids` in its error log.
+
 If one-shot analysis fails and closing its session also fails, the original
 error details remain inline and `details.cleanup_error` describes the later
 close failure. Each diagnostic retains its own reported resources; the later
@@ -601,6 +612,9 @@ Saved snapshots include only cache entries whose subject identifies the selected
 target. Unbound observations and observations of child artifacts remain available
 in the open session and its Evidence bundle; they are excluded from the target's
 saved replay entries without changing their subjects.
+The snapshot also retains available Evidence linked by selected records, including
+transitive sources with an unbound or different subject. Those sources are not
+replay entries for the selected target. Unrelated records remain excluded.
 
 Snapshots retain eligible target-scoped question histories in full, including
 mutation Evidence recorded while another target was active. Observations and

docs/client-configuration.md

@@ -45,6 +45,10 @@ 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).
 
+`rea doctor` has the same limit for provider checks, and reports a provider setting
+the registration's file does not carry as a
+[non-blocking unknown](installation.md#check-readiness-for-your-task).
+
 ## Runtime settings and client deadlines
 
 `update_analysis_settings` changes curated defaults inside the running REA

docs/elf-notes.md

@@ -38,6 +38,12 @@ were examined; an unavailable section name does not erase those note facts.
 For GNU notes, `gnu.build_id_hex`, `gnu.abi_tag`, or `gnu.gold_version` are
 filled when the descriptor matches that type. Other owners keep `gnu` null.
 
+For Linux `CORE` notes, `core.prpsinfo`, `core.file`, `core.siginfo`, or
+`core.auxv` are decoded for process arguments and status (`NT_PRPSINFO`), mapped
+file memory regions and paths (`NT_FILE`), fault signal and code (`NT_SIGINFO`), and
+auxiliary vectors (`NT_AUXV`) across 32-bit and 64-bit images. Other owners or unparsed
+notes keep `core` null.
+
 `PT_NOTE` and `SHT_NOTE` are examined independently. The same file range may
 appear twice when both tables declare it.
 
@@ -48,7 +54,7 @@ the image never carried notes in another container or overlay.
 
 The selected file is limited to 64 MiB by default (512 MiB maximum). At most
 32 note entries are examined by default across every table. Retained note
-names, section names, and GNU descriptor text share a scan budget based on
+names, section names, GNU descriptor text, and core dump string representations share a scan budget based on
 the source bytes plus any decoded section-name table, capped at
 `max_file_bytes`. The raw source and decoded table must also fit together
 within that ceiling. If admission fails, the error reports the required

docs/evm-bytecode.md

@@ -28,6 +28,15 @@ The host must already provide util-linux `prlimit`, normally `/usr/bin/prlimit`;
 no system tools and changes no user configuration. [Upstream provenance and
 license](https://github.com/morluto/rea/blob/main/third_party/evmole/README.md) are packaged.
 
+Limiter discovery validates the selected path without launching it. A relative
+path or directory is reported as `not_configured`, a missing file as
+`executable_missing`, and denied access or another filesystem-probe failure as
+`runtime_unavailable`. Recovery names the selected path and
+`REA_EVM_PRLIMIT_COMMAND`; denied access asks for execute permission and
+filesystem access. The original admission or system code stays in diagnostics.
+An available filesystem probe does not verify the selected tool's version or
+util-linux compatibility, and REA does not substitute another command.
+
 ## Evidence semantics
 
 - `encoding` is required: raw bytes or UTF-8 hex, with optional `0x` prefix and

docs/firmware-analysis.md

@@ -26,6 +26,9 @@ REA does not install these tools, their dependencies or system packages. It
 checks the tool's `--version` banner when executing a request. Binwalk must
 print `binwalk <version>` and Unblob must print the version alone. Inspection and
 extraction have independent prerequisites; one does not require the other.
+Capability discovery recommends `REA_BINWALK_COMMAND` for missing inspection
+and `REA_UNBLOB_COMMAND` for missing extraction. Configuring the other engine
+does not enable the unavailable operation.
 Both require util-linux `prlimit`, normally `/usr/bin/prlimit`; override its
 absolute path with `REA_FIRMWARE_PRLIMIT_COMMAND` if needed. `rea doctor` does
 not currently inspect firmware readiness. Engine selection/version checks run

docs/flutter-analysis.md

@@ -109,9 +109,13 @@ server; older servers keep the complete request after schema discovery.
   header check does not establish valid table contents or exported symbols.
 - **`libflutter` facts** are per-ABI observations: byte size, SHA-256
   digest, GNU build IDs from ELF-declared `PT_NOTE` / `SHT_NOTE` ranges,
-  and any _labeled_ strings the build
-  carries. Release engine builds often strip the `Dart VM version` string —
-  absence is reported as `null`, not guessed. Android clang/LLVM toolchain
+  and Dart/toolchain strings the build carries. `dart_version` accepts the
+  labeled `Dart VM version:` form and the unlabeled Dart
+  `Version::String()` form (`<version> (<channel>) (<commit time>)` with an
+  optional ` on "<os>_<arch>"` suffix) that release engines embed. An
+  unlabeled match is a candidate based on its shape; it is not bound to a
+  Dart symbol and another string can match. `null` means no supported pattern
+  was found, not proof that no version exists. Android clang/LLVM toolchain
   lines are reported verbatim as build provenance.
   `build_id_candidates` preserves distinct IDs. `build_id` is populated only
   when all declared note ranges were examined and one ID was found;
@@ -122,10 +126,13 @@ server; older servers keep the complete request after schema discovery.
   Compressed `SHT_NOTE` sections are skipped with an unsupported-compression
   limitation and partial coverage; IDs from other note ranges remain candidates.
   Encoded note storage is never interpreted as note headers or inflated.
-- Labeled strings must fit their complete grammar. `dart_version_capped`
-  and `toolchain_capped` independently report labels omitted by grammar or
-  projection bounds; either makes identification coverage partial. Values
-  split across read chunks are retained without publishing truncated prefixes.
+- Version and toolchain strings must fit their complete grammar.
+  `dart_version_capped` and `toolchain_capped` independently report labels
+  omitted by grammar or projection bounds; either makes identification
+  coverage partial. Values split across read chunks are retained without
+  publishing truncated prefixes. Unlabeled runs that miss the
+  `Version::String()` grammar are ignored and do not set
+  `dart_version_capped`.
 - **`coverage: "partial"`** also appears when an ABI carries `libapp.so`
   without `libflutter.so` (or vice versa).
 - The APK itself is digested before parsing, so `target.sha256` binds the

docs/index.md

@@ -51,7 +51,6 @@ For runtime instrumentation, see the [Frida guide](./frida-instrumentation.md).
 | --------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | Identify a desktop installation                     | [Runtime candidates, evidence and follow-up files](desktop-applications.md)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
 | Inspect native functions, references, or types      | [Native binaries](native-investigation.md), [Go metadata](go-binaries.md), [Rust dependencies](rust-binaries.md), [CPython pyc files](python-pyc.md), [PE certificates](pe-certificates.md), [PE imports](pe-imports.md), [PE TLS/load config](pe-load-config.md), [ELF notes](elf-notes.md), [Linux kernel modules](kernel-modules.md), [Apple IPS](apple-ips.md), [Erlang BEAM](erlang-beam.md), [offline ELF layout](binary-diagnostics.md), [recorded crashes](recorded-crashes.md)                                                                               |
-| 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), [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)                                                                                                                                                                                                                                                                                                                                                                |

docs/installation.md

@@ -390,6 +390,20 @@ A scoped report has `scope.mode: "explicit"`. Its `scope_checks` determine
 `environment_healthy` summarizes the full audit. `--target` adds a target check,
 but the report remains audit-wide unless a scope option is also supplied.
 
+Provider checks read the terminal running doctor. A client-started server may
+receive a different environment, and doctor cannot observe it. When an available
+provider relies on a setting that a registration's file does not record, or
+records with other text, doctor adds a non-blocking
+`registration_environment:<client>` check with `classification: "unknown"`. The
+setting names appear in that registration's `provider_settings`. Selecting the
+client or an affected provider places the check in `scope_checks`; it never
+changes `healthy`, because the client may still pass the setting on. Preview
+`rea setup --client <client-id> --skill=false --dry-run` from that terminal and
+approve it to record the settings, then restart the client. To see what the
+running server can use, call `binary_session` in the client and read
+`result.tool_availability`. For Hopper, only an explicit `HOPPER_LAUNCHER_PATH`
+is compared.
+
 An invalid `REA_LOG_LEVEL` fails every scope, including one client or the
 installed skill, because the executable rejects it before any command. A
 selected client also fails for every other setting that MCP startup rejects,

docs/javascript-artifact-reconstruction.md

@@ -876,8 +876,22 @@ and Evidence. If that expansion does not fit, the file node retains
 `static_analysis` and any admitted `semantic_module_analysis` observations,
 including their exact values and source locations. Use the public modules item
 view to read them. The graph marks those unexpanded relationships as unknown.
-If cumulative result capacity is exhausted, analysis stops; inventoried but
-unexamined files remain present with explicit unknown scopes.
+
+The parent charges everything it retains against the heap that was free when
+analysis started, less a transfer reserve. Semantic facts and expanded
+relationships stop at half of that capacity, and a source refused there keeps
+its static facts with the refusal reported. Static facts can continue to three
+quarters of it while the live heap also has room for another copy of what it
+holds, so results charged for earlier sources do not cost later sources their
+static facts when the heap can still hold them. When that share runs short,
+relationships that were reserved but not yet expanded are given up before any
+static facts, and each affected file reports the omission.
+
+If static facts themselves exhaust that share, or the parent's live heap cannot
+hold the next checkpoint, analysis stops; inventoried but unexamined files remain
+present with explicit unknown scopes. The failure reports the limit that applied
+in bytes, what was still available, the live heap in use and what the checkpoint
+needed.
 
 ### Large local JSON inputs
 

docs/javascript-runtime-reconciliation.md

@@ -93,6 +93,10 @@ coverage. It does not print captured source text.
 Runtime targets, frames, scripts, and workers become capture-scoped graph
 nodes. REA evaluates compatible static candidates conservatively:
 
+V8 Inspector targets whose protocol type is `node` use JavaScript asset/module
+candidates for their verified entry location. A target-only correspondence does
+not mark that script loaded; load-state evidence requires a script observation.
+
 1. A captured-source SHA-256 plus one matching mapped location yields
    a content-and-location match.
 2. When no static candidate exists at a mapped location, one unique exact

docs/kuna-provider.md

@@ -1,9 +1,27 @@
 # Kuna provider
 
-[Kuna](https://github.com/Noelo-Lab/kuna) is an Apache-2.0 decompiler distributed as one `kuna` executable. For a new installation, use Kuna 1.988, REA's recommended verified release. REA uses a `kuna` you supply; it does not download, install, update or bundle Kuna. REA accepts other releases, which it reports as unverified in `rea doctor` and in each analysis profile. The verified-release flag compares the reported version; it does not authenticate the executable. The 1.988 real-provider checks ran on macOS arm64; Linux and other hosts have not been verified with that release.
+[Kuna](https://github.com/Noelo-Lab/kuna) is an Apache-2.0 decompiler distributed as one `kuna` executable. For a new installation, use Kuna 1.990, REA's recommended verified release. REA uses a `kuna` you supply; it does not download, install, update or bundle Kuna. REA accepts other releases; `rea doctor` and analysis Evidence report them as unverified. Verification compares the reported version; it does not authenticate the executable. Analysis profiles retain the observed version and executable digest, independently of REA's current verified-release policy. The 1.990 real-provider checks ran on macOS arm64; Linux and other hosts have not been verified with that release.
 
 Kuna is static: it reads the selected image and never executes it.
 
+This profile change makes earlier Kuna analysis snapshots and resumable directory
+exports incompatible, even with the same Kuna executable. Keep the old files:
+their recorded Evidence remains historical. To continue analysis, open the
+binary without the old snapshot and save a new one, or choose a new export
+directory. Existing snapshot Evidence can be extracted from its
+`evidence_bundle` JSON member and imported as a separate Evidence bundle; that
+does not restore cached workflow entries or resume the old directory export.
+For example, using `jq` and a new output path:
+
+```bash
+jq -e '.evidence_bundle | select(type == "object")' old-snapshot.json > history.json
+rea evidence-import history.json --json
+```
+
+The CLI command validates the bundle in a one-shot session. To use the records
+in an MCP session, call `import_evidence_bundle` with the extracted file path.
+This validates the embedded bundle, not the rest of the snapshot container.
+
 ## Configure
 
 ```bash
@@ -30,6 +48,10 @@ completes. Cleanup retries keep both the observations and the exact file owner.
 | `REA_KUNA_TIMEOUT_MS`         | 120 s                                                                                                                                   | Deadline for one single-function decompile, and for the inventory run REA makes when the export ends without one.                                                                        |
 | `REA_KUNA_JOBS`               | 1                                                                                                                                       | `decompile-project --jobs`. 1 is Kuna's reference answer; more jobs finish sooner but lose callee-first prototypes, and change about 40–60% of function bodies on the measured binaries. |
 
+Pseudocode read from a parallel project export includes a prototype-context
+limitation in its Evidence, including in function dossiers and composed
+workflows. Early single-function results have their own source limitation.
+
 A single-function decompile, inventory, string, graph or xref run that exceeds its deadline fails as `provider_timeout`, naming the setting that owns the deadline and that raising it takes a restart. A project export that exceeds `REA_KUNA_PROJECT_TIMEOUT_MS` is an export failure instead: requests that need the export report `capability_unavailable` with the export's own retry guidance.
 
 Windows is not supported yet. Supported targets are ELF and thin Mach-O executables for x86-64, AArch64 and ARM; PE and universal Mach-O are rejected with a typed reason.

docs/mcp-contracts.md

@@ -218,6 +218,12 @@ Malformed provider replies return `unreadable_output` for
 `resolve_containing_procedure` before successful-result projection;
 cancellation and incomplete cleanup remain errors.
 
+For a procedure match, `procedure_references` with `direction: "incoming"` can
+provide the selected provider's reference kinds when supported. Its scope covers
+the procedure body, so compare target addresses when selecting references to the
+exact entry. It is a separate observation and does not establish runtime use or
+complete reference discovery.
+
 REA prepares complete MCP results within the pinned stdio client's 10 MiB
 receive-buffer budget, including both text and structured representations and
 room for the JSON-RPC envelope. Tool errors omit `structuredContent` from the
@@ -292,6 +298,12 @@ limitation and reason IDs index that page's `items.messages` dictionary. Expand
 those references to recover exact text, repeated messages, and absent versus
 empty optional fields. Failed nodes retain their original error.
 
+Retained `xrefs` Evidence also supports `native-observation` address pages and
+`native-context` source caveats. `xrefs` still returns complete Evidence by
+default and does not accept `detail`; when its MCP response exceeds the budget,
+follow the returned continuation to page the retained result. These addresses
+remain untyped; paging does not add reference kinds or establish completeness.
+
 These views reference complete source context through `source_context.digest`
 and caveat counts. Read it using the same parent with
 `view: {"kind":"native-context","facet":"overview"}`. The other facets are
@@ -371,6 +383,12 @@ is null. `total` counts all matching heads; each page preserves complete records
 in stable unknown ID order. Filters apply before paging. Pages reflect current
 session state, so keep the unknown ledger unchanged while traversing it.
 
+`list_unknowns` only lists registered heads. Import restores the Unknown records
+present in a bundle; it does not turn residual question text embedded in Evidence
+into registry entries. An empty registry therefore does not establish that
+retained Evidence has no open questions. Inspect the relevant Evidence or its
+analysis view for its residual questions.
+
 Automatically retained workflow questions include their immutable result
 Evidence ID. Distinct results retain independent questions and source links;
 repeating the same result does not create another unknown. Workflow Evidence
@@ -390,9 +408,26 @@ that revision. If a list response overflows, retry on the same connection with
 the same filters and offset and a smaller limit; export if one head still cannot
 fit.
 
+To find missing sources before a downstream analysis refuses them, read
+`missing_direct_links` from the summary, or call `get_evidence_bundle` with
+`detail: "links"`. The result (`kind: "evidence-link-inspection"`) transfers no
+record payload. `filters` select the starting records, while membership is
+checked against every record in the session or file, so a filtered-out source is
+`retained`, not missing. Rows (`evidence_id`, `linked_evidence_id`, `status`) are
+in canonical order, default to `link_status: "missing"` and page with `offset` and
+`limit` (default 64); `links` counts every inspected link regardless of that
+selection. `traversal: "direct"` (the default) reads the selected records' own
+links and sets `retained_closure` to null, because it makes no closure claim.
+`traversal: "retained-closure"` also follows retained links, as composed workflows
+such as `build_call_path` do, and reports `complete` or `incomplete`; anything
+beyond a missing link remains unknown. Missing means absent from this session or
+file, not nonexistent, and neither status describes analysis coverage. Importing
+a missing source changes this membership without changing any Evidence ID.
+
 For a portable exported bundle, the CLI shares this projection:
 `rea inspect-evidence-bundle '{"path":"/tmp/evidence.json","detail":"summary","filters":{"operation":"analyze_function"}}' --format json`.
-`"detail":"records"` with an `evidence_id` filter returns that complete record.
+`"detail":"records"` with an `evidence_id` filter returns that complete record,
+and `"detail":"links"` reads link membership.
 The CLI validates and materializes that local bundle under its existing memory
 budget; summary delivery does not make arbitrary large files cheap to import.
 

docs/native-investigation.md

@@ -300,6 +300,20 @@ relationships but reports their completeness as unknown. In particular, a resolv
 tail call observed in one direction does not prove that the reverse inventory is
 complete. An empty Hopper inventory cannot establish that no such call exists.
 No whole-binary reverse scan is performed.
+
+For large native traces, `trace_feature` accepts `detail: "summary"`. It retains
+the complete trace and returns counts and its parent Evidence ID. Use
+`inspect_analysis_view` with that ID and `view: {kind: "native-feature-trace",
+collection: "references", offset: 0, limit: 64}` to page the original rows;
+`matches` and `unknowns` are separate collections. Matches accept an exact
+`address`; references accept exact `source_address` and `target_address`
+filters. Row indices refer to the retained collection, and page coverage does not establish provider discovery
+completeness. `list_unknowns` pages the independently managed question heads.
+In the one-shot CLI, `rea trace ... --detail summary --evidence_output PATH`
+stores the trace and its linked source Evidence for later
+`inspect-analysis-view` calls. This bundle does not include the CLI session's
+Unknown registry; its original question texts remain available in the trace's
+`unknowns` pages.
 Regex searches use ECMAScript Unicode syntax in a cancellable worker with a
 matching deadline and a worker old-generation heap. Deadline or cancellation
 stops matching while leaving the Hopper API available. The deadline is
@@ -388,6 +402,11 @@ sites remain distinct. A static route does not establish runtime reachability.
 Swift/closure dispatch requires resolved static references; unavailable ABI
 forms remain unknown.
 
+Encoded Objective-C method records retain their own locations in dispatch
+Evidence. A handler node uses the implementation address with an unknown file
+offset unless that function already has an independently located graph node;
+the method-record offset does not locate the handler's code.
+
 Incomplete reference kinds do not discard known typed calls or partial
 provider call references. A `provider_call` with `observed` resolution retains
 the provider-reported call site and endpoint without claiming generic direct,
@@ -1004,7 +1023,9 @@ with a path-specific gap and incomplete capture coverage. Null alone does not
 establish that an accessibility value was successfully read or absent.
 
 An initial PID or window mismatch is `invalid_request` on `pid` or
-`window_id` and leaves provider availability intact. An unavailable executable
+`window_id` and leaves provider availability intact. A selected window that
+exists off screen is not a mismatch: selection succeeds and the permission and
+capture checks report their own outcome. An unavailable executable
 URL or unresolved executable path leaves identity unknown and reports
 `capability_unavailable`. Identity or window loss
 after the initial capture remains an observation failure with collected facts.

docs/readme/README_ar.md

@@ -20,6 +20,8 @@
 
 **[الموقع](https://rea.tools/ar/) · [الأدلة](https://rea.tools/ar/guides/) · [دراسات الحالة](https://rea.tools/ar/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="انضم إلى مجتمع REA على Discord" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [البدء السريع](#البدء-السريع) · [كيف يعمل REA](#كيف-يعمل-rea) · [ما الذي يمكنك تحليله](#ما-الذي-يمكنك-تحليله) · [دراسات الحالة](#دراسات-الحالة) · [إنشاء بيئات التعلم المعزز](#build-rl-environments) · [الأسئلة الشائعة](#الأسئلة-الشائعة) · [أدوات GNU objdump وRizin](../reverse-engineering-tools.md) · [التوثيق](#التوثيق)
 
 <code>npx rea-agents setup</code>

docs/readme/README_de.md

@@ -20,6 +20,8 @@
 
 **[Website](https://rea.tools/de/) · [Anleitungen](https://rea.tools/de/guides/) · [Fallstudien](https://rea.tools/de/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="Der REA-Community auf Discord beitreten" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [Schnellstart](#schnellstart) · [So funktioniert REA](#so-funktioniert-rea) · [Was du analysieren kannst](#was-du-analysieren-kannst) · [Fallstudien](#fallstudien) · [RL-Umgebungen erstellen](#build-rl-environments) · [Häufige Fragen](#häufige-fragen) · [Dokumentation](#dokumentation)
 
 <code>npx rea-agents setup</code>

docs/readme/README_el.md

@@ -19,6 +19,8 @@
 
 **[Ιστότοπος](https://rea.tools/) · [Οδηγοί](https://rea.tools/guides/) · [Μελέτες περίπτωσης](https://rea.tools/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="Έλα στην κοινότητα REA στο Discord" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [Γρήγορη εκκίνηση](#γρήγορη-εκκίνηση) · [Πώς λειτουργεί το REA](#πώς-λειτουργεί-το-rea) · [Τι μπορείς να αναλύσεις](#τι-μπορείς-να-αναλύσεις) · [Μελέτες περίπτωσης](#μελέτες-περίπτωσης) · [Δημιουργία περιβαλλόντων RL](#build-rl-environments) · [Συχνές ερωτήσεις](#συχνές-ερωτήσεις) · [Τεκμηρίωση](#τεκμηρίωση)
 
 <code>npx rea-agents setup</code>

docs/readme/README_es.md

@@ -20,6 +20,8 @@
 
 **[Sitio web](https://rea.tools/es/) · [Guías](https://rea.tools/es/guides/) · [Casos prácticos](https://rea.tools/es/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="Únete a la comunidad de REA en Discord" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [Inicio rápido](#inicio-rápido) · [Cómo funciona REA](#cómo-funciona-rea) · [Qué puedes analizar](#qué-puedes-analizar) · [Casos prácticos](#casos-prácticos) · [Crear entornos de RL](#build-rl-environments) · [Preguntas frecuentes](#preguntas-frecuentes) · [Documentación](#documentación)
 
 <code>npx rea-agents setup</code>

docs/readme/README_fa.md

@@ -20,6 +20,8 @@
 
 **[وب‌سایت](https://rea.tools/fa/) · [راهنماها](https://rea.tools/fa/guides/) · [نمونه‌های عملی](https://rea.tools/fa/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="به انجمن REA در دیسکورد بپیوندید" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [شروع سریع](#شروع-سریع) · [REA چگونه کار می‌کند؟](#rea-چگونه-کار-می‌کند) · [چه چیزهایی را میتوان تحلیل کرد؟](#چه-چیزهایی-را-می‌توان-تحلیل-کرد) · [نمونه‌های عملی](#نمونه‌های-عملی) · [ساخت محیط‌های RL](#build-rl-environments) · [پرسش‌های متداول](#پرسش‌های-متداول) · [مستندات](#مستندات)
 
 <code>npx rea-agents setup</code>

docs/readme/README_fr.md

@@ -20,6 +20,8 @@
 
 **[Site web](https://rea.tools/fr/) · [Guides](https://rea.tools/fr/guides/) · [Études de cas](https://rea.tools/fr/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="Rejoignez la communauté REA sur Discord" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [Démarrage rapide](#démarrage-rapide) · [Comment fonctionne REA](#comment-fonctionne-rea) · [Ce que vous pouvez analyser](#ce-que-vous-pouvez-analyser) · [Études de cas](#études-de-cas) · [Créer des environnements RL](#build-rl-environments) · [Questions fréquentes](#questions-fréquentes) · [Documentation](#documentation)
 
 <code>npx rea-agents setup</code>

docs/readme/README_id.md

@@ -20,6 +20,8 @@
 
 **[Situs Web](https://rea.tools/id/) · [Panduan](https://rea.tools/id/guides/) · [Contoh Penggunaan](https://rea.tools/id/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="Bergabunglah dengan komunitas REA di Discord" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [Mulai Cepat](#mulai-cepat) · [Cara Kerja REA](#cara-kerja-rea) · [Hal yang Dapat Anda Analisis](#hal-yang-dapat-anda-analisis) · [Contoh Penggunaan](#contoh-penggunaan) · [Membangun lingkungan RL](#build-rl-environments) · [FAQ](#faq) · [Dokumentasi](#dokumentasi)
 
 <code>npx rea-agents setup</code>

docs/readme/README_it.md

@@ -20,6 +20,8 @@
 
 **[Sito web](https://rea.tools/it/) · [Guide](https://rea.tools/it/guides/) · [Showcase](https://rea.tools/it/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="Unisciti alla community REA su Discord" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [Avvio rapido](#avvio-rapido) · [Come funziona REA](#come-funziona-rea) · [Cosa puoi analizzare](#cosa-puoi-analizzare) · [Showcase](#showcase) · [Creare ambienti RL](#build-rl-environments) · [FAQ](#faq) · [Documentazione](#documentazione)
 
 <code>npx rea-agents setup</code>

docs/readme/README_ja.md

@@ -20,6 +20,8 @@
 
 **[ウェブサイト](https://rea.tools/ja/) · [ガイド](https://rea.tools/ja/guides/) · [事例](https://rea.tools/ja/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="DiscordのREAコミュニティに参加" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [クイックスタート](#クイックスタート) · [REA の仕組み](#rea-の仕組み) · [分析できる対象](#分析できる対象) · [事例](#事例) · [RL 環境を構築する](#build-rl-environments) · [よくある質問](#よくある質問) · [ドキュメント](#ドキュメント)
 
 <code>npx rea-agents setup</code>

docs/readme/README_ko.md

@@ -20,6 +20,8 @@
 
 **[웹사이트](https://rea.tools/ko/) · [가이드](https://rea.tools/ko/guides/) · [사례](https://rea.tools/ko/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="Discord에서 REA 커뮤니티에 참여하세요" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [빠른 시작](#빠른-시작) · [REA의 작동 방식](#rea의-작동-방식) · [분석할 수 있는 대상](#분석할-수-있는-대상) · [사례](#사례) · [RL 환경 만들기](#build-rl-environments) · [자주 묻는 질문](#자주-묻는-질문) · [문서](#문서)
 
 <code>npx rea-agents setup</code>

docs/readme/README_ml.md

@@ -20,6 +20,8 @@
 
 **[വെബ്സൈറ്റ്](https://rea.tools/) · [ഗൈഡുകൾ](https://rea.tools/guides/) · [ഉദാഹരണങ്ങൾ](https://rea.tools/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="Discord-ൽ REA കമ്മ്യൂണിറ്റിയിൽ ചേരുക" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [ദ്രുതാരംഭം](#ദ്രുതാരംഭം) · [REA എങ്ങനെ പ്രവർത്തിക്കുന്നു](#rea-എങ്ങനെ-പ്രവർത്തിക്കുന്നു) · [എന്തൊക്കെ വിശകലനം ചെയ്യാം](#എന്തൊക്കെ-വിശകലനം-ചെയ്യാം) · [ഉദാഹരണങ്ങൾ](#ഉദാഹരണങ്ങൾ) · [RL പരിതസ്ഥിതികൾ നിർമ്മിക്കുക](#build-rl-environments) · [പതിവുചോദ്യങ്ങൾ](#പതിവുചോദ്യങ്ങൾ) · [ഡോക്യുമെന്റേഷൻ](#ഡോക്യുമെന്റേഷൻ)
 
 <code>npx rea-agents setup</code>

docs/readme/README_pl.md

@@ -20,6 +20,8 @@
 
 **[Strona internetowa](https://rea.tools/pl/) · [Przewodniki](https://rea.tools/pl/guides/) · [Przykłady zastosowań](https://rea.tools/pl/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="Dołącz do społeczności REA na Discordzie" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [Szybki start](#szybki-start) · [Jak działa REA](#jak-działa-rea) · [Co możesz analizować](#co-możesz-analizować) · [Przykłady zastosowań](#przykłady-zastosowań) · [Tworzenie środowisk RL](#build-rl-environments) · [FAQ](#faq) · [Dokumentacja](#dokumentacja)
 
 <code>npx rea-agents setup</code>

docs/readme/README_pt-BR.md

@@ -20,6 +20,8 @@
 
 **[Site](https://rea.tools/pt-BR/) · [Guias](https://rea.tools/pt-BR/guides/) · [Casos de uso](https://rea.tools/pt-BR/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="Participe da comunidade REA no Discord" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [Início rápido](#início-rápido) · [Como o REA funciona](#como-o-rea-funciona) · [O que você pode analisar](#o-que-você-pode-analisar) · [Casos de uso](#casos-de-uso) · [Criar ambientes de RL](#build-rl-environments) · [Perguntas frequentes](#perguntas-frequentes) · [Documentação](#documentação)
 
 <code>npx rea-agents setup</code>

docs/readme/README_ro.md

@@ -20,6 +20,8 @@
 
 **[Site web](https://rea.tools/) · [Ghiduri](https://rea.tools/guides/) · [Studii de caz](https://rea.tools/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="Alătură-te comunității REA pe Discord" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [Pornire rapidă](#pornire-rapidă) · [Cum funcționează REA](#cum-funcționează-rea) · [Ce poți analiza](#ce-poți-analiza) · [Studii de caz](#studii-de-caz) · [Construiește medii RL](#build-rl-environments) · [Întrebări frecvente](#întrebări-frecvente) · [Documentație](#documentație)
 
 <code>npx rea-agents setup</code>

docs/readme/README_ru.md

@@ -20,6 +20,8 @@
 
 **[Сайт](https://rea.tools/ru/) · [Руководства](https://rea.tools/ru/guides/) · [Примеры](https://rea.tools/ru/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="Присоединяйтесь к сообществу REA в Discord" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [Быстрый старт](#быстрый-старт) · [Как работает REA](#как-работает-rea) · [Что можно анализировать](#что-можно-анализировать) · [Примеры](#примеры) · [Создание RL-окружений](#build-rl-environments) · [Частые вопросы](#частые-вопросы) · [Документация](#документация)
 
 <code>npx rea-agents setup</code>

docs/readme/README_th.md

@@ -20,6 +20,8 @@
 
 **[เว็บไซต์](https://rea.tools/th/) · [คู่มือ](https://rea.tools/th/guides/) · [ตัวอย่างการใช้งาน](https://rea.tools/th/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="เข้าร่วมชุมชน REA บน Discord" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [เริ่มต้นอย่างรวดเร็ว](#เริ่มต้นอย่างรวดเร็ว) · [REA ทำงานอย่างไร](#rea-ทำงานอย่างไร) · [สิ่งที่วิเคราะห์ได้](#สิ่งที่วิเคราะห์ได้) · [ตัวอย่างการใช้งาน](#ตัวอย่างการใช้งาน) · [สร้างสภาพแวดล้อม RL](#build-rl-environments) · [คำถามที่พบบ่อย](#คำถามที่พบบ่อย) · [เอกสาร](#เอกสาร)
 
 <code>npx rea-agents setup</code>

docs/readme/README_tr.md

@@ -20,6 +20,8 @@
 
 **[Web sitesi](https://rea.tools/tr/) · [Rehberler](https://rea.tools/tr/guides/) · [Örnek çalışmalar](https://rea.tools/tr/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="Discord'da REA topluluğuna katılın" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [Hızlı başlangıç](#hızlı-başlangıç) · [REA nasıl çalışır](#rea-nasıl-çalışır) · [Neleri analiz edebilirsiniz](#neleri-analiz-edebilirsiniz) · [Örnek çalışmalar](#örnek-çalışmalar) · [RL ortamları oluşturun](#build-rl-environments) · [Sık sorulan sorular](#sık-sorulan-sorular) · [GNU objdump ve Rizin araçları](../reverse-engineering-tools.md) · [Belgeler](#belgeler)
 
 <code>npx rea-agents setup</code>

docs/readme/README_uk.md

@@ -20,6 +20,8 @@
 
 **[Сайт](https://rea.tools/uk/) · [Посібники](https://rea.tools/uk/guides/) · [Приклади](https://rea.tools/uk/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="Приєднуйтеся до спільноти REA в Discord" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [Швидкий старт](#швидкий-старт) · [Як працює REA](#як-працює-rea) · [Що можна аналізувати](#що-можна-аналізувати) · [Приклади](#приклади) · [Створення RL-середовищ](#build-rl-environments) · [Поширені запитання](#поширені-запитання) · [Документація](#документація)
 
 <code>npx rea-agents setup</code>

docs/readme/README_ur-Latn.md

@@ -20,6 +20,8 @@
 
 **[Website](https://rea.tools/) · [Guides](https://rea.tools/guides/) · [Showcases](https://rea.tools/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="Discord par REA community mein shamil hon" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [Jaldi shuru karein](#jaldi-shuru-karein) · [REA kaise kaam karta hai](#rea-kaise-kaam-karta-hai) · [Kya kuch analyze kar sakte hain](#kya-kuch-analyze-kar-sakte-hain) · [Amli misaalein](#amli-misaalein) · [RL environments banayein](#build-rl-environments) · [FAQ](#faq) · [Documentation](#documentation)
 
 <code>npx rea-agents setup</code>

docs/readme/README_vi.md

@@ -20,6 +20,8 @@
 
 **[Trang web](https://rea.tools/vi/) · [Hướng dẫn](https://rea.tools/vi/guides/) · [Các nghiên cứu điển hình](https://rea.tools/vi/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="Tham gia cộng đồng REA trên Discord" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [Bắt đầu nhanh](#bắt-đầu-nhanh) · [Cách REA hoạt động](#cách-rea-hoạt-động) · [Những gì bạn có thể phân tích](#những-gì-bạn-có-thể-phân-tích) · [Các nghiên cứu điển hình](#các-nghiên-cứu-điển-hình) · [Xây dựng môi trường RL](#build-rl-environments) · [Câu hỏi thường gặp](#câu-hỏi-thường-gặp) · [Tài liệu](#tài-liệu)
 
 <code>npx rea-agents setup</code>

docs/readme/README_zh-TW.md

@@ -20,6 +20,8 @@
 
 **[網站](https://rea.tools/zh-TW/) · [指南](https://rea.tools/zh-TW/guides/) · [案例](https://rea.tools/zh-TW/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="加入 REA 的 Discord 社群" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [快速開始](#快速開始) · [REA 的工作原理](#rea-的工作原理) · [可以分析什麼](#可以分析什麼) · [案例](#案例) · [建立 RL 環境](#build-rl-environments) · [常見問題](#常見問題) · [文件](#文件)
 
 <code>npx rea-agents setup</code>

docs/readme/README_zh.md

@@ -20,6 +20,8 @@
 
 **[网站](https://rea.tools/zh-CN/) · [指南](https://rea.tools/zh-CN/guides/) · [案例](https://rea.tools/zh-CN/showcase/)**
 
+<a href="https://discord.com/invite/GkcryMnJDM"><img alt="加入 REA 的 Discord 社区" src="https://img.shields.io/badge/Join%20us%20on%20Discord-5865F2?style=for-the-badge&logo=discord&logoColor=white" height="40"></a>
+
 [快速开始](#快速开始) · [REA 的工作原理](#rea-的工作原理) · [可以分析什么](#可以分析什么) · [案例](#案例) · [构建 RL 环境](#build-rl-environments) · [常见问题](#常见问题) · [GNU objdump 和 Rizin 工具](../reverse-engineering-tools.md) · [文档](#文档)
 
 <code>npx rea-agents setup</code>

docs/reverse-engineering-tools.md

@@ -14,7 +14,13 @@ can run.
 
 ## GNU objdump
 
-`inspect_with_objdump` and `rea inspect-with-objdump` capture stdout and stderr as inline Evidence. Artifact inspection Evidence records SHA-256 digests before and after the provider call and whether those observed digests differ; this cannot prove the exact bytes consumed if the artifact changes during execution. Choose one artifact operation: `file_headers`, `section_headers`, `symbols`, `relocations`, `dwarf`, `disassemble`, or `disassemble_all`. `disassemble` maps to `-d`; `disassemble_all` maps to `-D` and has different symbol-boundary semantics. The pathless `inspect_with_objdump {"operation":"architectures"}` MCP call or `rea list-objdump-architectures` CLI command maps to `-i` and produces subjectless provider-capability Evidence describing BFD targets compiled into the installed binary, not a guarantee that a target is supported.
+REA sends GNU-style arguments to the selected command but does not verify its
+implementation or version. Evidence identifies the command profile as
+`objdump.command` and retains the selected executable; it does not claim that
+the executable is GNU objdump. Other implementations may accept some commands
+while differing in supported options and output.
+
+`inspect_with_objdump` and `rea inspect-with-objdump` capture stdout and stderr as inline Evidence. Artifact inspection Evidence records SHA-256 digests before and after the provider call and whether those observed digests differ; this cannot prove the exact bytes consumed if the artifact changes during execution. Choose one artifact operation: `file_headers`, `section_headers`, `symbols`, `relocations`, `dwarf`, `disassemble`, or `disassemble_all`. `disassemble` maps to `-d`; `disassemble_all` maps to `-D` and has different symbol-boundary semantics. The pathless `inspect_with_objdump {"operation":"architectures"}` MCP call or `rea list-objdump-architectures` CLI command maps to `-i` and produces subjectless Evidence containing the selected command’s output, not a guarantee that any target is supported. GNU objdump uses this option to list its compiled-in BFD targets.
 
 Failure to launch the selected executable reports provider unavailability, the
 configured command and the host error under `boundary: "provider-launch"`.
@@ -25,7 +31,7 @@ their rejected fields in input issues before artifact reads or provider launch.
 
 For DWARF, REA does not follow local debug links by default. Set `follow_debug_links` to `true` to pass `-WK`; external debug-file identities are not bound to Evidence when following links is enabled. The CLI flag is `--follow-debug-links`; `--no-follow-debug-links` or `--follow-debug-links=false` keeps the default. A separate `true` or `false` word after the flag is not its value. REA clears `DEBUGINFOD_URLS` in the objdump child environment to disable debuginfod network access on GNU binutils versions that do not support `-WE`. The complete raw output is authoritative; REA does not normalize it into a version-independent disassembly schema.
 
-For a known native symbol, use `operation: "disassemble", symbol: "my_function"` in MCP or `--symbol my_function` in CLI. REA passes `--disassemble=my_function` to objdump before collecting output, rather than producing the whole disassembly and filtering it afterward. Omit `symbol` to keep full code-section disassembly. Other operations reject this selector. Use a nonempty, NUL-free name with well-formed Unicode; unsupported values are rejected before reading the artifact or starting objdump. Symbol names are passed unchanged; matching, versioned symbols, aliases and the end of the disassembly follow the installed GNU objdump's semantics. Evidence records the selector and actual arguments. An empty match does not establish artifact-wide absence, and the selected observation does not contain the omitted disassembly; request the complete operation when needed.
+For a known native symbol, use `operation: "disassemble", symbol: "my_function"` in MCP or `--symbol my_function` in CLI. REA passes `--disassemble=my_function` to objdump before collecting output, rather than producing the whole disassembly and filtering it afterward. Omit `symbol` to keep full code-section disassembly. Other operations reject this selector. Use a nonempty, NUL-free name with well-formed Unicode; unsupported values are rejected before reading the artifact or starting objdump. Symbol names are passed unchanged; matching, versioned symbols, aliases and the end of the disassembly follow the selected executable's semantics. Evidence records the selector and actual arguments. An empty match does not establish artifact-wide absence, and the selected observation does not contain the omitted disassembly; request the complete operation when needed.
 
 ```sh
 rea inspect-with-objdump ./program disassemble

docs/specs/agent-environments/fidelity-compare/spec.md

@@ -86,7 +86,10 @@ credentials and resets it between sequences.
   environment refused the call), `not-served`, `no-tool` and `unmapped-id`, each with a JSON pointer and short values.
 - The report gives agreement overall, per probe and per tool, agreement ignoring item order beside it, the counts per
   category, the ids mapped and the values normalised, the records left uncompared, and each step's differences (at most
-  20 per step).
+  20 per step). Each step gives `differences_total` before that cap, `differences_omitted`, and
+  `differences_truncated`, true when entries were omitted. Equality and categories use all differences.
+  Omitted entries are not retained and `--full-output` cannot recover them; further investigation uses the original
+  capture and probe Evidence.
 
 ## Non-goals
 

docs/testing-lanes.md

@@ -269,8 +269,8 @@ APK for the negative check. No engine or external tool is involved. Record:
 Flutter Gallery 2.9.2 (112 MB, arm64-v8a / armeabi-v7a / x86_64) — every
 ABI reports the same agreeing snapshot hash
 (`65817c30a78bb44c3dc3771876b6010a`, two sections each) read 20 bytes after
-the Dart snapshot magic, per-ABI engine GNU build-ids, no labeled Dart
-version string (expected for a release engine build), and the Android
+the Dart snapshot magic, per-ABI engine GNU build-ids, an unlabeled
+Dart-shaped version candidate, and the Android
 clang/LLVM toolchain line; the AOT inspection locates all four snapshot
 symbols through the dynamic symbol table on both ELF64 and ELF32 images,
 validates the data-section headers, agrees with the identification hash,
@@ -284,7 +284,7 @@ prefixes, with no private local-file dependency. The verifier now compares
 compiled CLI and stdio MCP Evidence on every ABI, including data-header kind
 and declared lengths. Add
 `--expectations scripts/fixtures/flutter-gallery-expectations.json` for the
-documented Gallery APK to assert its pinned digest, hash, exact engine labels
+documented Gallery APK to assert its pinned digest, hash, exact engine strings
 and per-ABI URI counts. The verifier requires complete structural snapshot
 coverage, reports bounded pool coverage as partial/unverified, and reports
 exact labels/counts on other APKs unverified without an expectations file.
@@ -421,7 +421,10 @@ the first cold pseudocode answer comes from a single-function run or an export
 that already finished, assembly waits for and serves from that export, and
 pseudocode and both dossier facets match their recorded file spans and digests,
 a fresh server reuses the export without rebuilding it, staging is empty after
-a completed export, and no owned process survives. Pass
+a completed export, and no owned process survives. A separate forced 1 ms
+project deadline checks that a timed-out inventory recommends raising the
+project deadline without changing jobs; a fresh server retries with 60 seconds
+and the same two-worker setting. Pass
 `--targets DIR --functions a,b` to add caller-built binaries laid out as
 `DIR/<flavor>/<name>` beside `<name>.stripped`; addresses come from the
 symbol-bearing build. `--compare-ghidra` with `GHIDRA_INSTALL_DIR` runs those
@@ -451,6 +454,16 @@ Mach-O fixture and caller-built symbol-bearing and stripped x86-64 ELF fixtures.
 Linux and other hosts have not been verified with 1.988; this is not a repeat
 of the larger 1.833 matrix.
 
+Kuna 1.989 passed the real-provider lane on macOS arm64 with the generated
+symbol-bearing and stripped Mach-O fixtures, including cold and warm reads,
+references, and cleanup. Linux, other hosts, and the larger 1.833 target matrix
+were not verified with 1.989.
+
+Kuna 1.990 passed the real-provider lane on macOS arm64 with the generated
+symbol-bearing and stripped Mach-O fixtures, including cold and warm reads,
+references, timeout recovery, and cleanup. Linux, other hosts, and the larger
+1.833 target matrix were not verified with 1.990.
+
 ## DOS Ghidra analysis
 
 `npm run verify:ghidra:dos` requires the supported Ghidra and JDK installation
@@ -1103,13 +1116,13 @@ coverage limits.
 ### Offline binary layout
 
 `npm run verify:binary:layout` requires Linux x64, GCC/binutils, the
-`i686-linux-gnu`, `arm-linux-gnueabi`, `mips-linux-gnu` and `mipsel-linux-gnu`
-cross `gcc`/`readelf` toolchains, absolute
+`aarch64-linux-gnu`, `i686-linux-gnu`, `arm-linux-gnueabi`, `mips-linux-gnu` and
+`mipsel-linux-gnu` cross `gcc`/`readelf` toolchains, absolute
 `REA_PWNTOOLS_PYTHON` with pwntools 4.15.0/pyelftools 0.33/Unicorn 2.1.2 and
 absolute `REA_VERIFY_STRACE_COMMAND`. It compiles ephemeral source-owned ELF
 fixtures and checks public CLI/MCP, lossless addresses/names, file ranges,
 mitigation inferences, malformed/unsupported input, original file hashes and
-released process ownership. Cross-compiled ELF32 executables and relocatable
+released process ownership. Cross-compiled ELF64 AArch64 and ELF32 executables and relocatable
 objects check the reported class, machine and byte order, and every section
 name, address, offset and size against GNU `readelf`. Exec syscall tracing must identify only the declared
 Node/Python launchers; no target binary is executed. Core/debugger claims need

docs/web-network-captures.md

@@ -97,9 +97,13 @@ it does not invent an empty string or body bytes.
 The observed Playwright 1.58.2 profile can report a bracketed IPv6
 `serverIPAddress`, forwarded from Chromium's `remoteIPAddress` through
 [Playwright's HAR tracer](https://github.com/microsoft/playwright/blob/v1.58.2/packages/playwright-core/src/server/har/harTracer.ts).
+Chromium DevTools exports (declared as `WebInspector` `537.36`, the frozen
+AppleWebKit version in Chromium's user agent) report the same bracketed form:
+[its HAR writer](https://github.com/ChromeDevTools/devtools-frontend/blob/63739e8ec45ca01b9e4be9b8b05946acdadd8f1f/front_end/models/har/Log.ts)
+strips the port but not the brackets.
 REA preserves the original spelling in reported Evidence and removes brackets
-only from its validation copy, only for this declared producer and a valid IPv6
-literal. Invalid addresses, bracketed IPv4, ports and zone identifiers remain
+only from its validation copy, only for these declared producers and a valid
+IPv6 literal. Invalid addresses, bracketed IPv4, ports and zone identifiers remain
 validation failures. Producer declarations do not authenticate origin.
 
 Native mitmproxy decoding requires a caller-supplied **mitmdump 12.2.3 on

docs/web-runtime.md

@@ -22,7 +22,7 @@ Results retain:
 - Main-document script inventory, exact session script IDs, resource start coordinates, sourceURL/source-map declarations, producer hash and independently computed UTF-8 text digest.
 - Armed-window requests from the selected main frame and selected origins, complete reported initiator objects (including stack hierarchy/descriptions), derived callsites, exact script-ID associations and unresolved async parent IDs. Source association does not establish UI causality. Callsite and listener `line_number`/`column_number` values are CDP's zero-based lines and UTF-16 columns in the resource named by `url`. With a `script_id`, that is the script's enclosing resource: the script file for an external script, or the HTML document for an inline script. `resource_start` is where the script text starts in that resource. A callsite with an empty `script_id` comes from the request's reported initiator rather than a script call frame, such as markup that the parser read in a document or a module import in a script file. It still locates a position in `url`, but has no session-script association, so it cannot be joined to captured source or `resource_start`. `trace_web_source_location` takes one-based, script-relative lines and zero-based UTF-16 columns.
 
-For an external script, where `url` is the script file, use `line = line_number + 1` and keep `column = column_number`; this also applies to an empty-`script_id` initiator position in a script file. For an inline script, which requires a `script_id` and its `resource_start`, use `line = line_number - resource_start.line_number + 1`. Subtract `resource_start.column_number` from `column_number` only when `line_number === resource_start.line_number`; keep the reported column on later lines. Columns remain zero-based. This conversion requires known source-start and column coordinates; preserve unavailable coordinates as unknown.
+For an external script, where `url` is the script file, use `line = line_number + 1` and keep `column = column_number`; this also applies to an empty-`script_id` initiator position in a script file. For an inline script, which requires a `script_id` and its `resource_start`, use `line = line_number - resource_start.line_number + 1`. Subtract `resource_start.column_number` from `column_number` only when `line_number === resource_start.line_number`; keep the reported column on later lines. Columns remain zero-based. This conversion requires known source-start and column coordinates; preserve unavailable coordinates as unknown. Chrome reports a negative start column for some inline scripts, such as one in a helper frame, and positions on that script's first line include it. REA keeps those columns as reported rather than failing the observation; a negative column does not locate a column in `url`, but the subtraction above still gives the script-relative column.
 
 The coverage counter interval starts at backend acceptance before the armed receipt and ends at the resetting sample after the local timer. Counts may include execution during these command intervals; request events are restricted to the locally armed window. The result retains both backend timestamps and the distinct local clock.
 

patches/release-please+17.3.0.patch

@@ -81,6 +81,51 @@
                  // In this case, there is no squashed merge commit. This could be a simple
                  // merge commit, a rebase merge commit, or a direct commit to the branch.
                  // Fallback to fetching the list of commits from the REST API. In the future
+@@ -1154,15 +1154,40 @@
+      * @returns {string} HTML URL of the new file
+      */
+     async createFileOnNewBranch(filename, contents, newBranchName, baseBranchName) {
+-        // create or update new branch to match base branch
+-        await this.forkBranch(newBranchName, baseBranchName);
+-        // use the single file upload API
++        // Preserve existing notes until the replacement file is committed.
++        // A failed write must not leave an open proposal pointing at a missing file.
++        if (!(await this.getBranchSha(newBranchName))) {
++            const baseSha = await this.getBranchSha(baseBranchName);
++            if (!baseSha) {
++                throw new Error(`Unable to find base branch: ${baseBranchName}`);
++            }
++            await this.createNewBranch(newBranchName, baseSha);
++        }
++        let existingSha;
++        try {
++            const { data } = await this.octokit.repos.getContent({
++                owner: this.repository.owner,
++                repo: this.repository.repo,
++                path: filename,
++                ref: newBranchName,
++            });
++            if (Array.isArray(data) || data.type !== 'file' || !data.sha) {
++                throw new Error(`Expected a file at ${filename} on branch: ${newBranchName}`);
++            }
++            existingSha = data.sha;
++        }
++        catch (error) {
++            if (!(error && error.status === 404)) {
++                throw error;
++            }
++        }
+         const { data: { content }, } = await this.octokit.repos.createOrUpdateFileContents({
+             owner: this.repository.owner,
+             repo: this.repository.repo,
+             path: filename,
+             // contents need to be base64 encoded
+-            content: Buffer.from(contents, 'binary').toString('base64'),
++            content: Buffer.from(contents, 'utf8').toString('base64'),
++            ...(existingSha ? { sha: existingSha } : {}),
+             message: 'Saving release notes',
+             branch: newBranchName,
+         });
 --- a/build/src/github.d.ts
 +++ b/build/src/github.d.ts
 @@ -47,6 +47,8 @@

scripts/ci/pr-readiness.d.mts

@@ -3,6 +3,7 @@ export interface ReadinessPullRequest {
   readonly state: "open" | "closed";
   readonly draft: boolean;
   readonly body: string | null;
+  readonly user: { readonly id: number } | null;
   readonly head: { readonly sha: string };
   readonly base: { readonly ref: string };
 }
@@ -53,7 +54,7 @@ export interface ReadinessGitHub {
   >;
 }
 export function evaluateReadiness(
-  pull: Pick<ReadinessPullRequest, "body" | "draft">,
+  pull: Pick<ReadinessPullRequest, "body" | "draft" | "user">,
   template: string,
 ): ReadinessResult;
 export function runReadinessCheck(input: {

scripts/ci/pr-readiness.mjs

@@ -2,6 +2,14 @@ import { readFile } from "node:fs/promises";
 
 const result = (state, description) => ({ state, description });
 
+// GitHub account IDs remain stable when a login changes.
+const EXEMPT_AUTHOR_IDS = new Set([
+  76467478, // morluto
+  208281322, // kaoru0822-kitauji
+  161784452, // N0zoM1z0
+  342580529, // gensokyo-dev
+]);
+
 const OPEN_HEADS_QUERY = `query ReadinessOpenHeads($owner: String!, $name: String!, $after: String) {
   repository(owner: $owner, name: $name) {
     pullRequests(first: 100, after: $after, states: OPEN, orderBy: {field: CREATED_AT, direction: ASC}) {
@@ -105,6 +113,11 @@ export function evaluateReadiness(pull, template) {
       "pending",
       "Draft PR: complete Author readiness before requesting review.",
     );
+  if (EXEMPT_AUTHOR_IDS.has(pull.user?.id))
+    return result(
+      "success",
+      "PR author is exempt from the readiness declaration.",
+    );
   const expected = readinessLines(template).flatMap((line) => {
     const match = /^- \[ \] (.+)$/u.exec(line);
     return match ? [match[1]] : [];
@@ -210,6 +223,7 @@ export async function runReadinessCheck({ github, context, core }) {
     latest.head.sha !== pull.head.sha ||
     latest.body !== pull.body ||
     latest.draft !== pull.draft ||
+    latest.user?.id !== pull.user?.id ||
     latest.base.ref !== pull.base.ref
   )
     verdict = result(

scripts/ci/scopes.mjs

@@ -76,6 +76,7 @@ const PATH_SCOPES = {
     "src/frida/frida-bindings.d.ts",
     "src/objdump/**",
     "src/cli/reverseEngineeringCommands.ts",
+    "src/process/ownedDebuggerCleanupError.ts",
     "src/process/ownedDebuggerSession.ts",
     "src/rizin/**",
     "src/contracts/*ToolContracts.ts",
@@ -103,6 +104,7 @@ const PATH_SCOPES = {
     "tests/boundary/providers/RizinInferiorTty.test.ts",
     "tests/boundary/providers/RizinTestInferiorTty.ts",
     "tests/boundary/process/ownedDebuggerSession.test.ts",
+    "tests/boundary/cli/debuggerOneShotExit.test.ts",
     "tests/boundary/cli/gdbStartupCleanupCli.test.ts",
     "tests/boundary/cli/reverseEngineeringCommands.test.ts",
     "tests/boundary/mcp/cutter*.test.ts",
@@ -163,6 +165,9 @@ const PATH_SCOPES = {
     "tests/boundary/mcp/nativeDemangleMcp.test.ts",
     "tests/boundary/mcp/nativeMachoSummaryMcp.test.ts",
     "tests/boundary/providers/native/nativeSignatureTargetBinding.test.ts",
+    "tests/boundary/providers/native/nativeUiOffscreenWindow.test.ts",
+    "tests/boundary/process/nativeUiVerifierLane.test.ts",
+    "tests/conformance/native/ui-offscreen.swift",
     "tests/boundary/cli/nativeSignatureCli.test.ts",
     "tests/boundary/cli/nativeMachoArm64_32Cli.test.ts",
     "tests/boundary/cli/nativeMachoEncryptionCli.test.ts",
@@ -699,7 +704,9 @@ export const CI_LANES = {
   agentenv: sameJobs(PATH_SCOPES.agentenv, ["agentenv"]),
   nativeaot: sameJobs(PATH_SCOPES.nativeaot, ["nativeaot"]),
   ghidra_bridge: sameJobs(PATH_SCOPES.ghidra_bridge, ["ghidra_bridge"]),
-  website: sameJobs(PATH_SCOPES.website, ["website"]),
+  website: sameJobs(PATH_SCOPES.website, ["website"], {
+    earlyInputs: [".agents/skills/reverse-engineer-anything/**"],
+  }),
 };
 // An input owner omitted from the registry must never silently lose a lane.
 for (const [name, paths] of Object.entries(PATH_SCOPES))

scripts/fixtures/flutter-gallery-expectations.json

@@ -3,19 +3,19 @@
   "snapshot_hash": "65817c30a78bb44c3dc3771876b6010a",
   "engines": {
     "x86_64": {
-      "dart_version": null,
+      "dart_version": "2.14.0-151.0.dev (dev) (Tue May 25 10:58:39 2021 -0700)",
       "toolchain_lines": [
         "Android (5900059 based on r365631c) clang version 9.0.8 (https://android.googlesource.com/toolchain/llvm-project 207d7abc1a2abf3ef8d4301736d6a7ebc224a290) (based on LLVM 9.0.8svn)"
       ]
     },
     "armeabi-v7a": {
-      "dart_version": null,
+      "dart_version": "2.14.0-151.0.dev (dev) (Tue May 25 10:58:39 2021 -0700)",
       "toolchain_lines": [
         "Android (5900059 based on r365631c) clang version 9.0.8 (https://android.googlesource.com/toolchain/llvm-project 207d7abc1a2abf3ef8d4301736d6a7ebc224a290) (based on LLVM 9.0.8svn)"
       ]
     },
     "arm64-v8a": {
-      "dart_version": null,
+      "dart_version": "2.14.0-151.0.dev (dev) (Tue May 25 10:58:39 2021 -0700)",
       "toolchain_lines": [
         "Android (5900059 based on r365631c) clang version 9.0.8 (https://android.googlesource.com/toolchain/llvm-project 207d7abc1a2abf3ef8d4301736d6a7ebc224a290) (based on LLVM 9.0.8svn)"
       ]

scripts/lib/kuna-reference-verifier.mjs

@@ -114,6 +114,46 @@ export const verifyKunaReferences = async ({
         );
       }
       assert.equal(trace.value.truncated, false);
+      const summary = await call("trace_feature", {
+        query: name,
+        detail: "summary",
+      });
+      assert.equal(
+        summary.value.parent_evidence_id,
+        trace.structured.evidence_id,
+      );
+      assert.equal(
+        summary.value.summary.references,
+        trace.value.references.length,
+      );
+      assert.equal(
+        summary.value.summary.unknowns,
+        trace.value.residual_unknowns.length,
+      );
+      for (const [collection, values] of [
+        ["matches", trace.value.matches],
+        ["references", trace.value.references],
+        ["unknowns", trace.value.residual_unknowns],
+      ]) {
+        const view = await call("inspect_analysis_view", {
+          source: {
+            kind: "retained-evidence",
+            evidence_id: trace.structured.evidence_id,
+          },
+          view: {
+            kind: "native-feature-trace",
+            collection,
+            offset: 0,
+            limit: 1,
+          },
+        });
+        assert.equal(view.value.coverage.total, values.length);
+        assert.deepEqual(
+          view.value.items.rows.map(({ value }) => value),
+          values.slice(0, 1),
+        );
+        assert.equal(view.value.items.collection, collection);
+      }
     }
     composed = {
       graph_ms: graph.ms,

scripts/lib/native-value-e2e.mjs

@@ -253,20 +253,9 @@ async function verifyNativeValueAdapters(
       functionEvidence.analysis_profile,
     );
     assert.deepEqual(functionProfile, upstreamProfile);
-    const comparison = await client.callTool(
-      {
-        name: "compare_functions",
-        arguments: {
-          left: analyzed.structuredContent,
-          right: analyzed.structuredContent,
-        },
-      },
-      { timeout: 180000 },
-    );
-    assert.notEqual(comparison.isError, true, JSON.stringify(comparison));
-    assert.notEqual(comparison.structuredContent, undefined);
-    const comparisonEvidence = parseEvidence(
-      requireMcpOutput(comparison, "compare_functions"),
+    const comparisonEvidence = await compareRetainedFunctionEvidence(
+      client,
+      functionEvidence,
     );
     assert.equal(
       comparisonEvidence.normalized_result.status,
@@ -395,21 +384,27 @@ async function verifyUnresolvedCallEvidence(client) {
   assert.equal(trace.goal_status, "unknown");
   assert.equal(trace.truncated, true);
   assert.ok(trace.residual_unknowns.length > 0);
+  const compared = await compareRetainedFunctionEvidence(client, evidence);
+  assert.equal(compared.normalized_result.status, "unknown");
+}
+
+/** Compare an already admitted function record without retransmitting its payload. */
+export async function compareRetainedFunctionEvidence(client, evidence) {
+  const reference = {
+    kind: "retained-evidence",
+    evidence_id: evidence.evidence_id,
+  };
   const compared = await client.callTool(
     {
       name: "compare_functions",
       arguments: {
-        left: analyzed.structuredContent,
-        right: analyzed.structuredContent,
+        left: reference,
+        right: reference,
       },
     },
     { timeout: 180000 },
   );
   assert.notEqual(compared.isError, true, JSON.stringify(compared));
   assert.notEqual(compared.structuredContent, undefined);
-  assert.equal(
-    parseEvidence(requireMcpOutput(compared, "compare_functions"))
-      .normalized_result.status,
-    "unknown",
-  );
+  return parseEvidence(requireMcpOutput(compared, "compare_functions"));
 }

scripts/lib/release-proposal.d.mts

@@ -1,5 +1,7 @@
 export function applyReleasePleasePatch(directory?: string): Promise<void>;
 
+export function describeReleaseProposalError(error: unknown): string;
+
 export function releaseProposalSearchDepth(
   run: (command: string, args: string[]) => Promise<string>,
   sourceSha: string,

scripts/lib/release-proposal.mjs

@@ -13,6 +13,15 @@ const patch = fileURLToPath(
   new URL("../../patches/release-please+17.3.0.patch", import.meta.url),
 );
 
+export function describeReleaseProposalError(error) {
+  if (!(error instanceof Error)) return String(error);
+  const description = error.message || error.name || "Unknown error";
+  const status = error.status;
+  return Number.isInteger(status) && status >= 400 && status <= 599
+    ? `${description} (HTTP ${status})`
+    : description;
+}
+
 export async function applyReleasePleasePatch(
   directory = dirname(require.resolve("release-please/package.json")),
 ) {

scripts/prepare-website.py

@@ -7,6 +7,7 @@ import xml.etree.ElementTree as ET
 from zipfile import ZIP_DEFLATED, ZipFile, ZipInfo
 
 from website import PageMetadata, page_url
+from website_agents import prepare_discovery, prepare_markdown
 
 
 EXAMPLE_FILES = (
@@ -81,6 +82,8 @@ def prepare_assets(site):
     prepare_sharing_image(site)
     prepare_sitemap(site)
     prepare_notes_example(site)
+    prepare_discovery(Path(__file__).resolve().parent.parent, site)
+    prepare_markdown(site)
 
 
 if __name__ == "__main__":

scripts/release-proposal.mjs

@@ -4,6 +4,7 @@ import { appendFile } from "node:fs/promises";
 import { parseArgs, promisify } from "node:util";
 import {
   applyReleasePleasePatch,
+  describeReleaseProposalError,
   releaseProposalSearchDepth,
 } from "./lib/release-proposal.mjs";
 
@@ -63,7 +64,7 @@ async function main() {
 
 await main().catch((error) => {
   process.stderr.write(
-    `Release proposal failed: ${error instanceof Error ? error.message : String(error)}\n`,
+    `Release proposal failed: ${describeReleaseProposalError(error)}\n`,
   );
   process.exitCode = 1;
 });

scripts/test-website-agents.py

@@ -0,0 +1,109 @@
+"""Check the public build artifacts and Markdown content contract."""
+
+import hashlib
+import json
+from pathlib import Path
+import tempfile
+import unittest
+from zipfile import ZipFile
+
+from bs4 import BeautifulSoup
+import yaml
+
+from website_agents import prepare_discovery, prepare_markdown
+
+
+ROOT = Path(__file__).resolve().parent.parent
+
+
+class AgentPublishingChecks(unittest.TestCase):
+    def test_published_skill_digest_covers_every_reference_and_catalogs_resolve(self):
+        site = ROOT / "website/_site"
+        index = json.loads((site / ".well-known/agent-skills/index.json").read_text())
+        self.assertEqual(index["$schema"], "https://schemas.agentskills.io/discovery/0.2.0/schema.json")
+        skill, = index["skills"]
+        self.assertEqual(skill["name"], "reverse-engineer-anything")
+        self.assertEqual(skill["type"], "archive")
+        artifact = site / skill["url"].removeprefix("https://rea.tools/")
+        self.assertEqual(skill["digest"], "sha256:" + hashlib.sha256(artifact.read_bytes()).hexdigest())
+        source = ROOT / ".agents/skills/reverse-engineer-anything"
+        with ZipFile(artifact) as archive:
+            expected = {f"{source.name}/{p.relative_to(source).as_posix()}": p.read_bytes()
+                        for p in source.rglob("*.md")}
+            self.assertEqual(set(archive.namelist()), set(expected))
+            for name, data in expected.items():
+                self.assertEqual(archive.read(name), data)
+            manifest = archive.read(f"{source.name}/SKILL.md").decode()
+            metadata = yaml.safe_load(manifest[4:].split("\n---\n", 1)[0])
+            self.assertEqual(skill["description"], metadata["description"])
+        catalog = json.loads((site / ".well-known/ai-catalog.json").read_text())
+        self.assertEqual(catalog["specVersion"], "1.0")
+        entry, = catalog["entries"]
+        self.assertEqual(entry["identifier"], "urn:air:rea.tools:skill:reverse-engineer-anything")
+        self.assertEqual(entry["url"], skill["url"])
+        self.assertNotIn("data", entry)
+        ard = json.loads((site / ".well-known/ard.json").read_text())
+        resource, = ard["entries"]
+        self.assertEqual(resource["url"], skill["url"])
+        self.assertTrue(2 <= len(resource["representativeQueries"]) <= 5)
+
+    def test_reference_changes_invalidate_digest_and_yaml_scalars_are_parsed(self):
+        with tempfile.TemporaryDirectory() as directory:
+            root = Path(directory)
+            source = root / ".agents/skills/reverse-engineer-anything"
+            source.mkdir(parents=True)
+            (source / "SKILL.md").write_text(
+                '---\nname: reverse-engineer-anything\ndescription: >-\n  Inspect programs:\n  preserve evidence.\n---\n# REA\n'
+            )
+            (source / "references").mkdir()
+            reference = source / "references/evidence.md"
+            reference.write_text("First revision")
+            site = root / "site"
+            def build():
+                prepare_discovery(root, site)
+                return json.loads((site / ".well-known/agent-skills/index.json").read_text())["skills"][0]
+            before = build()
+            self.assertEqual(before["description"], "Inspect programs: preserve evidence.")
+            self.assertEqual(build(), before)
+            reference.write_text("Second revision")
+            self.assertNotEqual(build()["digest"], before["digest"])
+
+    def test_markdown_preserves_content_and_resources_without_publishing_excluded_pages(self):
+        with tempfile.TemporaryDirectory() as directory:
+            site = Path(directory)
+            page = site / "zh-CN/guides/test/index.html"
+            page.parent.mkdir(parents=True)
+            page.write_text('''<html><head><title>REA: test</title></head><body>
+              <nav>Outside navigation</nav><main><aside>Shortened display paths.</aside>
+              <h1>Inspect a program</h1><nav>Contents navigation</nav>
+              <ol><li><span class="flow-label">Read</span><span class="flow-node"><code>input.exe</code></span><span class="flow-note">Keep evidence.</span></li></ol>
+              <p><a href="../other/?q=a%2Fb#code">Another guide</a></p>
+              <pre><code>const value = a &lt; b ? "x_y" : "&amp;";\n  keepIndent();</code></pre>
+              <details><summary>Evidence</summary><p>Hidden evidence remains available.</p></details>
+              <img src="../../../assets/diagram.svg" alt="Investigation diagram">
+              <button>Copy code</button><script>doNotPublish()</script></main></body></html>''')
+            fixture = site / "examples/notes-web/index.html"
+            fixture.parent.mkdir(parents=True)
+            fixture.write_text("<main>Target application</main>")
+            fallback = site / "zh-CN/fallback/index.html"
+            fallback.parent.mkdir(parents=True)
+            fallback.write_text('<head><meta name="robots" content="noindex, follow"></head><main>English fallback notice.</main>')
+            prepare_markdown(site)
+            markdown = page.with_suffix(".md").read_text()
+            self.assertIn('# Inspect a program', markdown)
+            self.assertIn('const value = a < b ? "x_y" : "&";\n  keepIndent();', markdown)
+            self.assertIn("Hidden evidence remains available.", markdown)
+            self.assertIn("Shortened display paths.", markdown)
+            self.assertNotIn("Read`input.exe`", markdown)
+            self.assertIn("https://rea.tools/zh-CN/guides/other/?q=a%2Fb#code", markdown)
+            self.assertIn("https://rea.tools/assets/diagram.svg", markdown)
+            for text in ("Outside navigation", "Contents navigation", "Copy code", "doNotPublish"):
+                self.assertNotIn(text, markdown)
+            self.assertFalse(fixture.with_suffix(".md").exists())
+            self.assertFalse(fallback.with_suffix(".md").exists())
+            html = BeautifulSoup(page.read_text(), "html.parser")
+            self.assertEqual(html.find("link", rel="alternate")["href"], "https://rea.tools/zh-CN/guides/test/index.md")
+
+
+if __name__ == "__main__":
+    unittest.main()

scripts/verify-binary-layout.mjs

@@ -38,15 +38,16 @@ if (
   !isAbsolute(strace ?? "")
 )
   throw new Error(
-    "verify:binary:layout requires Linux x64, absolute REA_PWNTOOLS_PYTHON (pwntools 4.15.0/pyelftools 0.33/Unicorn 2.1.2) and REA_VERIFY_STRACE_COMMAND. gcc, ld, strip and the i686/ARM/MIPS/MIPSel linux-gnu cross gcc and readelf must be available. No target is executed.",
+    "verify:binary:layout requires Linux x64, absolute REA_PWNTOOLS_PYTHON (pwntools 4.15.0/pyelftools 0.33/Unicorn 2.1.2) and REA_VERIFY_STRACE_COMMAND. gcc, ld, strip and the AArch64/i686/ARM/MIPS/MIPSel linux-gnu cross gcc and readelf must be available. No target is executed.",
   );
 const run = createVerifierRun();
 const execute = promisify(execFile);
-const ELF32_TOOLCHAINS = [
-  ["i686-linux-gnu", "EM_386", "little"],
-  ["arm-linux-gnueabi", "EM_ARM", "little"],
-  ["mips-linux-gnu", "EM_MIPS", "big"],
-  ["mipsel-linux-gnu", "EM_MIPS", "little"],
+const CROSS_TOOLCHAINS = [
+  ["aarch64-linux-gnu", "EM_AARCH64", 64, "little"],
+  ["i686-linux-gnu", "EM_386", 32, "little"],
+  ["arm-linux-gnueabi", "EM_ARM", 32, "little"],
+  ["mips-linux-gnu", "EM_MIPS", 32, "big"],
+  ["mipsel-linux-gnu", "EM_MIPS", 32, "little"],
 ];
 for (const command of [
   "gcc",
@@ -54,7 +55,7 @@ for (const command of [
   "strip",
   "/usr/bin/prlimit",
   strace,
-  ...ELF32_TOOLCHAINS.flatMap(([prefix]) => [
+  ...CROSS_TOOLCHAINS.flatMap(([prefix]) => [
     `${prefix}-gcc`,
     `${prefix}-readelf`,
   ]),
@@ -347,14 +348,15 @@ try {
       cases++;
     }
   }
-  // ELF32 profiles: cross-compiled, never executed, checked against GNU readelf.
+  // Cross profiles: cross-compiled, never executed, checked against GNU readelf.
   for (const [
     prefix,
     machine,
+    bits,
     byteOrder,
     kind,
     flags,
-  ] of ELF32_TOOLCHAINS.flatMap((toolchain) => [
+  ] of CROSS_TOOLCHAINS.flatMap((toolchain) => [
     [...toolchain, "executable", ["-fPIE", "-pie"]],
     [...toolchain, "relocatable", ["-c", "-fPIC"]],
   ])) {
@@ -423,16 +425,18 @@ try {
         `readelf relocation count: ${name}`,
       );
       for (const [entryIndex, [, offset, info]] of rows.entries()) {
-        // ELF32 r_info uses the low byte for type and the upper 24 bits for
-        // the symbol index. readelf has already decoded the file's byte order.
+        // ELF32 r_info packs an 8-bit type under a 24-bit symbol index;
+        // ELF64 packs a 32-bit type under a 32-bit index. readelf has already
+        // decoded the file's byte order.
         const decodedInfo = BigInt(`0x${info}`);
+        const typeBits = bits === 32 ? 8n : 32n;
         expectedRelocations.push({
           section_index: section.index,
           entry_index: entryIndex,
           reported_offset: BigInt(`0x${offset}`),
-          type: Number(decodedInfo & 0xffn),
+          type: Number(decodedInfo & ((1n << typeBits) - 1n)),
           symbol_table_index: section.link,
-          symbol_index: Number(decodedInfo >> 8n),
+          symbol_index: Number(decodedInfo >> typeBits),
         });
       }
     }
@@ -445,7 +449,7 @@ try {
       const value = await inspect(mode, path);
       assert.deepEqual(value.architecture, {
         machine,
-        bits: 32,
+        bits,
         byte_order: byteOrder,
       });
       assert.equal(
@@ -1312,7 +1316,8 @@ try {
       }
     }
   }
-  unsupported.writeUInt16LE(183, 18);
+  // EM_RISCV: AArch64 (183) is now an admitted profile.
+  unsupported.writeUInt16LE(243, 18);
   const core = Buffer.from(object);
   core.writeUInt16LE(4, 16);
   for (const [name, bytes, category] of [
@@ -1337,7 +1342,7 @@ try {
       "invalid_input",
     ],
     ["undersized-program-header", undersizedProgramHeader, "invalid_input"],
-    ["arm64", unsupported, "unsupported_target"],
+    ["riscv64", unsupported, "unsupported_target"],
     ["core", core, "unsupported_target"],
   ]) {
     const path = join(root.path, name);

scripts/verify-native-ui.mjs

@@ -245,7 +245,13 @@ try {
     scope,
     { environment: process.env },
   );
-  if (mismatch.ok || !mismatch.error.message.includes("target-mismatch"))
+  // A selection failure carries its helper code in the issue, not in its message.
+  if (
+    mismatch.ok ||
+    !mismatch.error.issues?.some(({ message }) =>
+      message.startsWith("target-mismatch:"),
+    )
+  )
     throw new Error("Real helper did not reject changed target bytes");
   report = {
     ok: true,

scripts/verify-real-kuna.mjs

@@ -28,7 +28,10 @@ import { StdioClientTransport } from "@modelcontextprotocol/client/stdio";
 import { inspectKunaInstallation } from "../dist/kuna/KunaInstallation.js";
 import { ArtifactResourceScope } from "../dist/artifacts/ArtifactResourceScope.js";
 import { AnalysisCleanupLease } from "../dist/artifacts/AnalysisCleanupLease.js";
-import { requireMcpOperationResult } from "./lib/mcp-verifier-results.mjs";
+import {
+  requireMcpOperationResult,
+  requireMcpToolError,
+} from "./lib/mcp-verifier-results.mjs";
 import { verifyKunaReferences } from "./lib/kuna-reference-verifier.mjs";
 import {
   nativeKunaStrings,
@@ -172,7 +175,7 @@ const sampleTree = async (root) => {
 };
 
 /** One MCP server with a selected provider, sampled while it runs. */
-const openServer = async (provider) => {
+const openServer = async (provider, kunaSettings = {}) => {
   const owner = Symbol(provider.id);
   pendingServers.add(owner);
   const transport = new StdioClientTransport({
@@ -185,6 +188,7 @@ const openServer = async (provider) => {
       REA_PROCESS_RUN_ID: run.run_id,
       REA_KUNA_COMMAND: kuna,
       REA_KUNA_CACHE_DIR: cacheRoot,
+      ...kunaSettings,
       ...(process.env.GHIDRA_INSTALL_DIR === undefined
         ? {}
         : { GHIDRA_INSTALL_DIR: process.env.GHIDRA_INSTALL_DIR }),
@@ -229,6 +233,13 @@ const openServer = async (provider) => {
       structured: result.structuredContent,
     };
   };
+  const callError = async (name, arguments_ = {}) => {
+    const result = await client.callTool(
+      { name, arguments: arguments_ },
+      { timeout: 3_600_000 },
+    );
+    return requireMcpToolError(result);
+  };
   const close = async (priorFailure) => {
     clearInterval(timer);
     await sample();
@@ -270,7 +281,59 @@ const openServer = async (provider) => {
     // A rejected connection/target still owns its transport and workspace.
     await close(cause);
   }
-  return { call, close };
+  return { call, callError, close };
+};
+
+/** Verify a forced inventory timeout can be retried without changing jobs. */
+const verifyProjectTimeoutRecovery = async (path, address) => {
+  const before = createHash("sha256")
+    .update(await readFile(path))
+    .digest("hex");
+  const settings = {
+    REA_KUNA_JOBS: "2",
+    REA_KUNA_TIMEOUT_MS: "60000",
+    REA_KUNA_PROJECT_TIMEOUT_MS: "1",
+  };
+  const timed = await openServer({ path, id: "kuna" }, settings);
+  let timedFailure;
+  try {
+    const failure = await timed.callError("procedure_assembly", {
+      procedure: address,
+    });
+    assert.equal(failure.code, "capability_unavailable");
+    assert.match(failure.message, /kuna functions/u);
+    assert.match(failure.remediation.action, /REA_KUNA_PROJECT_TIMEOUT_MS/u);
+    assert.doesNotMatch(failure.remediation.action, /REA_KUNA_JOBS/u);
+  } catch (cause) {
+    timedFailure = cause;
+  } finally {
+    await timed.close(timedFailure);
+  }
+  const retry = await openServer(
+    { path, id: "kuna" },
+    { ...settings, REA_KUNA_PROJECT_TIMEOUT_MS: "60000" },
+  );
+  let retryFailure;
+  try {
+    const assembly = await retry.call("procedure_assembly", {
+      procedure: address,
+    });
+    assert.equal(typeof assembly.value, "string");
+    assert.ok(assembly.value.length > 0);
+    assert.equal(assembly.structured.analysis_profile.parameters.jobs, 2);
+  } catch (cause) {
+    retryFailure = cause;
+  } finally {
+    await retry.close(retryFailure);
+  }
+  assert.equal(
+    createHash("sha256")
+      .update(await readFile(path))
+      .digest("hex"),
+    before,
+    "Kuna timeout recovery changed the target",
+  );
+  return { forced_deadline_ms: 1, retry_deadline_ms: 60000, jobs: 2 };
 };
 
 /** Count structuring and diagnostic markers in provider pseudocode. */
@@ -535,6 +598,7 @@ const verifyVariant = async ({ flavor, directory, symbols }, variant) => {
 };
 
 const results = [];
+let timeoutRecovery;
 const failures = [];
 let inspectionResourcesClean = true;
 try {
@@ -596,6 +660,11 @@ try {
       }),
     });
 
+  timeoutRecovery = await verifyProjectTimeoutRecovery(
+    built,
+    fixtureFunctions.get("rea_checksum"),
+  );
+
   // Caller-built matrix.
   for (const pair of callerPairs)
     for (const variant of [pair.file, `${pair.file}.stripped`])
@@ -650,6 +719,9 @@ const report = {
   platform: `${process.platform}/${process.arch}`,
   verifier_run: lifecycle,
   results,
+  ...(timeoutRecovery === undefined
+    ? {}
+    : { timeout_recovery: timeoutRecovery }),
   limitations: [
     "Targets are analyzed statically; they are never executed.",
     "Memory is the sampled peak resident set of the MCP server process tree; CPU is its sampled cumulative time. A short-lived peak between 200 ms samples is not observed.",

scripts/website.py

@@ -327,8 +327,9 @@ def main():
             refresh_contributors(root)
         elif args.command == "check":
             sync_pages(root, check=True)
-            for name in ("prepare-website.py", "verify-website.py", "test-website.py"):
+            for name in ("prepare-website.py", "verify-website.py", "test-website.py", "test-website-agents.py"):
                 run_script(root, name)
+            subprocess.run(["node", "--test", "website/worker.test.mjs"], cwd=root, check=True)
         elif args.command == "links":
             run_script(root, "audit-website-links.py", ["--report", args.report] if args.report else [])
         else:

scripts/website_agents.py

@@ -0,0 +1,116 @@
+"""Build public agent discovery and Markdown from their maintained sources."""
+
+import hashlib
+import json
+from urllib.parse import urljoin
+from zipfile import ZIP_DEFLATED, ZipFile, ZipInfo
+
+from bs4 import BeautifulSoup
+from markdownify import MarkdownConverter
+import yaml
+
+from website import NOTES_FIXTURES, PageMetadata, SITE_ORIGIN, page_url
+
+
+def write_json(path, value):
+    path.parent.mkdir(parents=True, exist_ok=True)
+    path.write_text(json.dumps(value, ensure_ascii=False, indent=2) + "\n", encoding="utf-8")
+
+
+def prepare_discovery(root, site):
+    """Publish the complete skill, including its relative reference documents."""
+    source = root / ".agents/skills/reverse-engineer-anything"
+    skill = (source / "SKILL.md").read_text(encoding="utf-8")
+    if not skill.startswith("---\n") or "\n---\n" not in skill[4:]:
+        raise ValueError("Public REA skill needs YAML frontmatter")
+    metadata = yaml.safe_load(skill[4:].split("\n---\n", 1)[0])
+    if not isinstance(metadata, dict):
+        raise ValueError("Public REA skill needs YAML metadata")
+    name, description = metadata["name"], metadata["description"]
+    if name != source.name or not isinstance(description, str) or not description.strip():
+        raise ValueError("Invalid public REA skill metadata")
+    discovery = site / ".well-known/agent-skills"
+    discovery.mkdir(parents=True, exist_ok=True)
+    artifact = discovery / f"{name}.zip"
+    with ZipFile(artifact, "w") as archive:
+        for path in [source / "SKILL.md", *sorted(source.glob("references/**/*.md"))]:
+            relative = path.relative_to(source)
+            entry = ZipInfo(f"{name}/{relative.as_posix()}", (1980, 1, 1, 0, 0, 0))
+            entry.create_system = 3
+            entry.external_attr = 0o100644 << 16
+            archive.writestr(entry, path.read_bytes(), compress_type=ZIP_DEFLATED)
+    artifact_url = f"{SITE_ORIGIN}/.well-known/agent-skills/{artifact.name}"
+    write_json(discovery / "index.json", {
+        "$schema": "https://schemas.agentskills.io/discovery/0.2.0/schema.json",
+        "skills": [{
+            "name": name, "type": "archive", "description": description,
+            "url": artifact_url,
+            "digest": "sha256:" + hashlib.sha256(artifact.read_bytes()).hexdigest(),
+        }],
+    })
+    entry = {
+        "identifier": f"urn:air:rea.tools:skill:{name}",
+        "displayName": "REA reverse engineering skill",
+        "description": description,
+        "type": "application/zip",
+        "url": artifact_url,
+    }
+    write_json(site / ".well-known/ai-catalog.json", {
+        "specVersion": "1.0",
+        "host": {"displayName": "REA", "documentationUrl": f"{SITE_ORIGIN}/get-started/"},
+        "entries": [entry],
+    })
+    write_json(site / ".well-known/ard.json", {"entries": [{
+        **entry,
+        "representativeQueries": [
+            "Explain how a feature works in a shipped executable using REA.",
+            "Trace an Electron application's behavior back to its packaged JavaScript.",
+            "Build an AgentEnv bundle from a web application capture.",
+        ],
+    }]})
+    print("Prepared agent skill archive, discovery index, AI Catalog and ARD manifest.")
+
+
+def prepare_markdown(site):
+    """Convert rendered reading pages, keeping code and resolving resource URLs."""
+    converter = MarkdownConverter(heading_style="ATX", bullets="-", escape_underscores=False)
+    count = 0
+    for path in sorted(site.rglob("*.html")):
+        if path.relative_to(site).as_posix() in NOTES_FIXTURES:
+            continue
+        source = path.read_text(encoding="utf-8")
+        metadata = PageMetadata()
+        metadata.feed(source)
+        # Drafts and English fallbacks keep their HTML indexing policy intact.
+        if metadata.noindex:
+            continue
+        soup = BeautifulSoup(source, "html.parser")
+        main = soup.find("main")
+        if main is None:
+            continue
+        # Preserve fallback notices and closed disclosures; remove interface chrome.
+        for node in main.select('script, style, nav, button, svg, .home-page-nav, [aria-hidden="true"]'):
+            if node.parent is not None:
+                node.decompose()
+        # These spans are separate lines in the shared flow component's CSS.
+        for node in main.select("span.flow-label, span.flow-node, span.flow-note"):
+            node.name = "div"
+        canonical = page_url(site, path)
+        for node in main.select("[href], [src]"):
+            for attribute in ("href", "src"):
+                if node.has_attr(attribute):
+                    node[attribute] = urljoin(canonical, node[attribute])
+        title = metadata.titles[0] if metadata.titles else "REA"
+        header = yaml.safe_dump({"title": title, "url": canonical}, allow_unicode=True, sort_keys=False)
+        markdown = converter.convert_soup(main).strip()
+        path.with_suffix(".md").write_text(f"---\n{header}---\n\n{markdown}\n", encoding="utf-8")
+        alternate = page_url(site, path.with_suffix(".md"))
+        links = (
+            f'<link rel="alternate" type="text/markdown" href="{alternate}" />\n'
+            f'<link rel="ard" type="application/json" href="{SITE_ORIGIN}/.well-known/ard.json" />\n'
+            f'<link rel="ai-catalog" type="application/ai-catalog+json" href="{SITE_ORIGIN}/.well-known/ai-catalog.json" />\n'
+            f'<link rel="related" type="application/json" title="Agent skills index" href="{SITE_ORIGIN}/.well-known/agent-skills/index.json" />\n'
+        )
+        path.write_text(source.replace("</head>", links + "</head>", 1), encoding="utf-8")
+        count += 1
+    print(f"Prepared Markdown for {count} reading pages.")

src/application/CapabilityInventory.test.ts

@@ -880,6 +880,62 @@ describe("trace_feature requirements", () => {
   });
 });
 
+describe("firmware operation recovery", () => {
+  it.each([
+    [false, false],
+    [true, false],
+    [false, true],
+    [true, true],
+  ])(
+    "keeps inspection=%s and extraction=%s independent",
+    (inspection, extraction) => {
+      const inventory = buildCapabilityInventory(status(), {
+        processCaptureEnabled: false,
+        firmwareInspectionEnabled: inspection,
+        firmwareExtractionEnabled: extraction,
+      });
+      for (const [name, enabled, command, otherCommand] of [
+        [
+          "inspect_firmware_regions",
+          inspection,
+          "REA_BINWALK_COMMAND",
+          "REA_UNBLOB_COMMAND",
+        ],
+        [
+          "extract_firmware",
+          extraction,
+          "REA_UNBLOB_COMMAND",
+          "REA_BINWALK_COMMAND",
+        ],
+      ] as const) {
+        const tool = inventory.find((candidate) => candidate.name === name);
+        expect(tool).toMatchObject({
+          available: enabled,
+          reason: enabled ? "available" : "provider_missing",
+        });
+        if (enabled) {
+          expect(tool?.remediation).toBeNull();
+        } else {
+          expect(tool?.remediation).toContain(command);
+          expect(tool?.remediation).not.toContain(otherCommand);
+          expect(tool?.remediation).toContain("prlimit");
+          expect(tool?.remediation).toContain("procps ps");
+          expect(tool?.remediation?.includes("external extractor")).toBe(
+            name === "extract_firmware",
+          );
+        }
+      }
+      const byName = (left: ToolAvailability, right: ToolAvailability) =>
+        left.name.localeCompare(right.name);
+      expect(
+        expandToolAvailability(compactToolAvailability(inventory)).toSorted(
+          byName,
+        ),
+      ).toEqual(inventory.toSorted(byName));
+    },
+  );
+});
+
 const HOST_RESTRICTED_TOOLS = [
   ["inspect_packet_capture", "packetCapture", "packetCaptureEnabled"],
   ["inspect_packet_fields", "packetCapture", "packetCaptureEnabled"],

src/application/CapabilityInventory.ts

@@ -1,6 +1,9 @@
 import { PCAP_CAPTURE_UNSUPPORTED_HOST_REASON } from "../domain/pcap/pcapAnalysis.js";
 import { DEFAULT_CALL_RELATIONSHIP_DIRECTION } from "../contracts/enhancedInputs.js";
-import { FIRMWARE_TOOL_REQUIREMENTS } from "../contracts/firmware/firmwareToolRequirements.js";
+import {
+  FIRMWARE_OPERATION_ENGINES,
+  FIRMWARE_TOOL_REQUIREMENTS,
+} from "../contracts/firmware/firmwareToolRequirements.js";
 import { CALL_RELATIONSHIP_TRAVERSALS } from "./CallRelationshipTraversal.js";
 import { NATIVE_DISPATCH_METADATA_SOURCES } from "./native/NativeDispatchMetadataInspection.js";
 import { NATIVE_UI_ACTION_OPERATIONS } from "./native/NativeUiActionTrace.js";
@@ -595,15 +598,19 @@ const workflowAvailabilityFor = ({
       "On Linux x64, set absolute REA_PWNTOOLS_PYTHON to caller-supplied Python with pwntools 4.15.0. No active binary target is required.",
     );
   if (kind === "firmware-provider") {
-    const { binwalk, unblob } = FIRMWARE_TOOL_REQUIREMENTS;
     const inspection = name === "inspect_firmware_regions";
+    const operation = inspection
+      ? "inspect_firmware_regions"
+      : "extract_firmware";
+    const requirement =
+      FIRMWARE_TOOL_REQUIREMENTS[FIRMWARE_OPERATION_ENGINES[operation]];
     return hostRestrictedAvailability(
       policy,
       inspection ? "firmwareInspection" : "firmwareExtraction",
       inspection
         ? policy.firmwareInspectionEnabled
         : policy.firmwareExtractionEnabled,
-      `On Linux, provide an absolute ${binwalk.commandEnvironment} (${binwalk.name} ${binwalk.line}, verified with ${binwalk.version}) or ${unblob.commandEnvironment} (${unblob.name} ${unblob.line}, verified with ${unblob.version}) path and util-linux prlimit. Extraction also requires the selected format’s external extractor.`,
+      `On Linux, provide an absolute ${requirement.commandEnvironment} (${requirement.requirement}) path, util-linux prlimit and procps ps.${inspection ? "" : " Extraction also requires the selected format’s external extractor."}`,
     );
   }
   if (kind === "android-provider")

src/application/ClientRegistrationEnvironment.ts

@@ -127,6 +127,62 @@ export const clientRegistrationEnvironmentDetails = (
   return validatedDetails(environment, validation, platform);
 };
 
+/** Setting names a registration does not carry as the value selected here. */
+export interface RecordedProviderSettings {
+  /** Selected here and absent from the registration's recorded environment. */
+  readonly unrecorded: readonly string[];
+  /** Recorded with text other than the value selected here. */
+  readonly differing: readonly string[];
+  /** Recorded as an expression, or in a map REA could not read. */
+  readonly unresolved: readonly string[];
+}
+
+/**
+ * Compare settings selected in this process with a registration's own file.
+ * The server's environment also depends on what its client passes on, which is
+ * not observable here, so a gap is never a claim about the effective value.
+ * Returns only names: recorded values stay in the file that owns them.
+ */
+export const recordedProviderSettings = (
+  parsed: ClientConfigurationDocument,
+  selected: Readonly<Record<string, string>>,
+  platform: NodeJS.Platform = process.platform,
+): RecordedProviderSettings | undefined => {
+  const names = Object.keys(selected).sort(compareUnicodeCodePoints);
+  if (names.length === 0) return undefined;
+  const details = clientRegistrationEnvironmentDetails(
+    parsed,
+    {},
+    "fragment",
+    platform,
+  );
+  if (!details.ok) return { unrecorded: [], differing: [], unresolved: names };
+  const recorded = snapshotEnvironment(details.value.values, platform);
+  // Expression names fold like every other environment name on this platform.
+  const expressions = snapshotEnvironment(
+    Object.fromEntries(
+      [...details.value.unresolvedSettings].map((name) => [name, ""]),
+    ),
+    platform,
+  );
+  const facts = {
+    unrecorded: names.filter(
+      (name) => recorded[name] === undefined && expressions[name] === undefined,
+    ),
+    differing: names.filter(
+      (name) =>
+        recorded[name] !== undefined && recorded[name] !== selected[name],
+    ),
+    unresolved: names.filter((name) => expressions[name] !== undefined),
+  };
+  return facts.unrecorded.length +
+    facts.differing.length +
+    facts.unresolved.length ===
+    0
+    ? undefined
+    : facts;
+};
+
 /** Resolve the async provider-specific budget through its retained reader owner. */
 export const clientRegistrationEnvironmentDetailsWithBudget = async (
   parsed: ClientConfigurationDocument | undefined,

src/application/ClientRegistrationStatus.ts

@@ -34,8 +34,14 @@ import {
 import type { SetupClient } from "./SupportedClients.js";
 import { compareUnicodeCodePoints } from "../domain/unicodeCodePointOrder.js";
 import { dshDocument } from "./DshCordisPatch.js";
-import { clientRegistrationEnvironmentDetailsWithBudget } from "./ClientRegistrationEnvironment.js";
-import type { ProviderRequestBudgetResolver } from "./ClientRegistrationEnvironment.js";
+import {
+  clientRegistrationEnvironmentDetailsWithBudget,
+  recordedProviderSettings,
+} from "./ClientRegistrationEnvironment.js";
+import type {
+  ProviderRequestBudgetResolver,
+  RecordedProviderSettings,
+} from "./ClientRegistrationEnvironment.js";
 import type { ArtifactResourceScope } from "../artifacts/ArtifactResourceScope.js";
 
 import {
@@ -52,6 +58,8 @@ interface ClientRegistrationStatusBase {
   readonly package_reference?: string;
   /** Non-blocking timeout guidance; caller-selected values remain aligned. */
   readonly advisory?: string;
+  /** Provider settings this process selected that the registration's file does not carry. */
+  readonly provider_settings?: RecordedProviderSettings;
 }
 
 type RegistrationCommand = readonly [string, ...string[]];
@@ -99,6 +107,8 @@ interface ClientRegistrationReadOptions {
    */
   readonly evidence?: "readiness" | "ownership";
   readonly resolveProviderRequestBudget?: ProviderRequestBudgetResolver;
+  /** Settings to compare with each registration's file; omitted skips that read. */
+  readonly providerSettings?: Readonly<Record<string, string>>;
 }
 
 /** Registration facts shared by diagnostics and update maintenance. */
@@ -362,6 +372,13 @@ export const readClientRegistrationInspections = async (
                 registrationEnvironment.value.timeoutInputs,
               )
             : undefined,
+          options.providerSettings === undefined
+            ? undefined
+            : recordedProviderSettings(
+                parsed,
+                options.providerSettings,
+                options.platform,
+              ),
         ),
         activation,
         commandFacts.identity,
@@ -494,6 +511,7 @@ const configuredStatus = (
   policyRemediation?: string,
   packageReference?: string,
   advisory?: string,
+  providerSettings?: RecordedProviderSettings,
 ): ClientRegistrationStatus =>
   state === "aligned"
     ? {
@@ -506,6 +524,9 @@ const configuredStatus = (
         state,
         remediation: null,
         ...(advisory === undefined ? {} : { advisory }),
+        ...(providerSettings === undefined
+          ? {}
+          : { provider_settings: providerSettings }),
       }
     : {
         client: client.name,
@@ -516,6 +537,9 @@ const configuredStatus = (
           : { package_reference: packageReference }),
         state,
         remediation: policyRemediation ?? remediation(client),
+        ...(providerSettings === undefined
+          ? {}
+          : { provider_settings: providerSettings }),
       };
 
 const timeoutAdvisory = (

src/application/DirectAnalysis.ts

@@ -18,7 +18,14 @@ import { silentLogger } from "../logger.js";
 import type { Logger } from "pino";
 import { withEvidenceCallerInputPath } from "../domain/evidence.js";
 import { createImmutableEvidenceBundle } from "../domain/evidenceBundle.js";
-import { retainAnalysisResultSources } from "./investigation/recordEvidenceSources.js";
+import {
+  retainAnalysisResultSources,
+  type AnalysisResultWithSources,
+} from "./investigation/recordEvidenceSources.js";
+import {
+  createInvestigationEvidenceClosureChecker,
+  resolveInvestigationEvidenceClosure,
+} from "./investigation/InvestigationEvidence.js";
 import type { Evidence } from "../domain/evidence.js";
 import type { NativeToolName } from "../contracts/native/nativeToolContracts.js";
 import type { EnhancedToolName } from "../contracts/enhancedInputs.js";
@@ -139,13 +146,17 @@ export const runDirectAnalysis = async (
     readonly architecture?: BinaryArchitecture;
     readonly entryPoint?: string;
     readonly espFlash?: EspFlashSelection;
+    readonly includeEvidenceSources?: boolean;
   } = {},
-): Promise<Result<Evidence, JsonValue>> =>
+): Promise<AnalysisResultWithSources<Evidence, JsonValue>> =>
   withProcessCancellation(options.signal, (signal) =>
     runAnalysis(dependencies, path, tool, arguments_, {
       logger: options.logger ?? silentLogger,
       snapshotPath: options.snapshotPath,
       signal,
+      ...(options.includeEvidenceSources
+        ? { includeEvidenceSources: true }
+        : {}),
       ...targetSelection(options),
       ...(options.providerId === undefined
         ? {}
@@ -365,13 +376,14 @@ const runAnalysis = async (
     readonly signal: AbortSignal;
     readonly evidenceParameters?: Readonly<Record<string, JsonValue>>;
     readonly createSession?: () => BinarySession | Promise<BinarySession>;
+    readonly includeEvidenceSources?: boolean;
     readonly providerId?: AnalysisProviderSelector;
     readonly formatHint?: ExecutableFormatHint;
     readonly architecture?: BinaryArchitecture;
     readonly entryPoint?: string;
     readonly espFlash?: EspFlashSelection;
   },
-): Promise<Result<Evidence, JsonValue>> => {
+): Promise<AnalysisResultWithSources<Evidence, JsonValue>> => {
   const { logger, signal, snapshotPath } = options;
   const evidenceParameters = options.evidenceParameters ?? arguments_;
   let session: BinarySession;
@@ -387,6 +399,29 @@ const runAnalysis = async (
     )(config.value, logger);
   }
   let publishedSnapshot: PublishedEvidenceFile | undefined;
+  let sourceEvidence: readonly Evidence[] | undefined;
+  const captureSources = (
+    evidence: Evidence,
+    supplied: readonly Evidence[] = [],
+  ): Result<null, AnalysisError> => {
+    if (!options.includeEvidenceSources) return ok(null);
+    const records = new Map(
+      supplied.map((record) => [record.evidence_id, record]),
+    );
+    const captured = new Map<string, Evidence>();
+    const closure = resolveInvestigationEvidenceClosure(
+      {
+        evidenceForAnalysis: (id) => {
+          const record = records.get(id) ?? session.evidenceForAnalysis(id);
+          if (record !== undefined) captured.set(id, record);
+          return record;
+        },
+      },
+      evidence.evidence_links,
+    );
+    sourceEvidence = [...captured.values()];
+    return closure.ok ? ok(null) : closure;
+  };
   const execute = async (): Promise<Result<Evidence, AnalysisError>> => {
     let isDirectory = false;
     if (BUNDLE_RESOURCE_OPERATIONS.has(tool)) {
@@ -458,8 +493,29 @@ const runAnalysis = async (
             : routeProviderIdentity(route, tool),
           evidenceProfile,
         });
-        if (cached !== undefined)
-          return ok(withEvidenceCallerInputPath(cached, path));
+        if (cached !== undefined) {
+          if (cached.evidence_links.length === 0)
+            return ok(withEvidenceCallerInputPath(cached, path));
+          const records = new Map(
+            snapshot.evidence_bundle.records.map((record) => [
+              record.evidence_id,
+              record,
+            ]),
+          );
+          const checkClosure = createInvestigationEvidenceClosureChecker({
+            evidenceForAnalysis: (id) => records.get(id),
+          });
+          if (checkClosure(cached.evidence_links)) {
+            const evidence = withEvidenceCallerInputPath(cached, path);
+            const captured = captureSources(
+              evidence,
+              snapshot.evidence_bundle.records,
+            );
+            if (!captured.ok)
+              return err(captured.error.retainPartialObservation(evidence));
+            return ok(evidence);
+          }
+        }
       }
     }
     const openOptions = {
@@ -496,6 +552,9 @@ const runAnalysis = async (
     );
     if (!recorded.ok)
       return err(recorded.error.retainPartialObservation(evidence));
+    const captured = captureSources(evidence);
+    if (!captured.ok)
+      return err(captured.error.retainPartialObservation(evidence));
     if (isWorkflowEvidenceTool(tool)) {
       const unknowns = recordWorkflowUnknowns({
         name: tool,
@@ -575,11 +634,15 @@ const runAnalysis = async (
       outcome.cleanupError.retainDiagnostics({
         analysis_snapshot: { ...publishedSnapshot },
       });
-    return err(
-      directAnalysisCleanupFailure(result, outcome.cleanupError, path),
-    );
+    return {
+      ...err(directAnalysisCleanupFailure(result, outcome.cleanupError, path)),
+      ...(sourceEvidence === undefined ? {} : { sourceEvidence }),
+    };
   }
-  return result.ok ? ok(result.value) : err(cliError(result.error, path));
+  return {
+    ...(result.ok ? ok(result.value) : err(cliError(result.error, path))),
+    ...(sourceEvidence === undefined ? {} : { sourceEvidence }),
+  };
 };
 
 const executeAnalysisTool = async (input: {

src/application/Doctor.ts

@@ -57,6 +57,7 @@ import {
   type UnhealthyClientRegistrationStatus,
 } from "./ClientRegistrationStatus.js";
 import type { ProviderRequestBudgetResolver } from "./ClientRegistrationEnvironment.js";
+import { registrationSpelledSettings } from "./SetupRegistrationEnvironment.js";
 import {
   collectDoctorDiagnostics,
   doctorHealthy,
@@ -146,6 +147,7 @@ export interface DoctorHost {
   close?(): Promise<string | undefined>;
   clientRegistrations?(
     selectedClientIds?: readonly string[],
+    providerSettings?: Readonly<Record<string, string>>,
   ): Promise<readonly ClientRegistrationStatus[]>;
   ilspyCmdVersion?(path: string): Promise<string | undefined>;
 }
@@ -276,18 +278,26 @@ const inspectDoctor = async (
     hopperPath,
     providerInspections,
   } = await collectDoctorDiagnostics(target, host);
-  const identity = await collectDoctorIdentity(host, scope);
+  const hopperAvailable =
+    hopperPath !== undefined &&
+    diagnosticChecks
+      .filter(({ name }) => name.startsWith("hopper"))
+      .every(({ ok }) => ok);
+  const selections = providerSettingSelections(
+    providerInspections,
+    hopperAvailable && hopperPath === host.configuredHopperPath
+      ? hopperPath
+      : undefined,
+  );
+  const identity = await collectDoctorIdentity(host, scope, selections);
   const checks = [
     ...diagnosticChecks,
     ...identity.checks,
     ...registrationAdvisoryChecks(identity.value.registrations),
+    ...registrationEnvironmentChecks(identity.value.registrations, selections),
   ];
   const providers = {
-    hopperAvailable:
-      hopperPath !== undefined &&
-      checks
-        .filter(({ name }) => name.startsWith("hopper"))
-        .every(({ ok }) => ok),
+    hopperAvailable,
     hopperConfigured: host.configuredHopperPath !== undefined,
     providerInspections,
   };
@@ -329,6 +339,77 @@ const registrationAdvisoryChecks = (
         ],
   );
 
+/** Settings an available provider's checks in this report relied on. */
+interface ProviderSettingSelection {
+  readonly provider: string;
+  readonly settings: Readonly<Record<string, string>>;
+}
+
+const providerSettingSelections = (
+  inspections: readonly DoctorProviderInspection[] | undefined,
+  configuredHopperPath: string | undefined,
+): readonly ProviderSettingSelection[] => [
+  ...(inspections ?? [])
+    .filter(({ available }) => available)
+    .map(({ id, registrationEnvironment }) => ({
+      provider: id,
+      settings: registrationEnvironment,
+    })),
+  // Startup probes the fixed and renamed locations on its own, so only an
+  // explicit path is something this terminal selected for the server.
+  ...(configuredHopperPath === undefined
+    ? []
+    : [
+        {
+          provider: "hopper",
+          settings: { HOPPER_LAUNCHER_PATH: configuredHopperPath },
+        },
+      ]),
+];
+
+/**
+ * A healthy provider check describes this terminal, not the server a client
+ * starts. Report what the registration's file leaves out without gating health:
+ * the client may still pass the setting on, which doctor cannot observe.
+ */
+const registrationEnvironmentChecks = (
+  registrations: readonly ClientRegistrationStatus[],
+  selections: readonly ProviderSettingSelection[],
+): readonly DoctorCheck[] =>
+  registrations.flatMap(({ client, provider_settings: settings }) => {
+    if (settings === undefined) return [];
+    const { unrecorded, differing, unresolved } = settings;
+    const names = [...unrecorded, ...differing, ...unresolved];
+    return [
+      {
+        name: `registration_environment:${client}`,
+        ok: true,
+        classification: "unknown" as const,
+        detail: [
+          `Provider checks used this terminal's environment; what the server ${client} starts receives is unknown.`,
+          ...(unrecorded.length === 0
+            ? []
+            : [`Its registration does not record ${unrecorded.join(", ")}.`]),
+          ...(differing.length === 0
+            ? []
+            : [`It records other values for ${differing.join(", ")}.`]),
+          ...(unresolved.length === 0
+            ? []
+            : [`REA could not resolve its ${unresolved.join(", ")}.`]),
+        ].join(" "),
+        details: {
+          effective_environment: "unknown",
+          providers: selections
+            .filter(({ settings: selected }) =>
+              names.some((name) => selected[name] !== undefined),
+            )
+            .map(({ provider }) => provider),
+        },
+        remediation: `Preview rea setup --client ${client} --skill=false --dry-run from this terminal, apply it to record these settings and restart the client, or read binary_session result.tool_availability in the client.`,
+      },
+    ];
+  });
+
 const closeDoctorHost = async (
   host: DoctorHost,
 ): Promise<string | AnalysisError | undefined> => {
@@ -369,12 +450,19 @@ const doctorReportWithCleanup = (
 const collectDoctorIdentity = async (
   host: DoctorHost,
   scope: DoctorScopeReport,
+  selections: readonly ProviderSettingSelection[],
 ): Promise<{
   readonly checks: readonly DoctorCheck[];
   readonly value: DoctorIdentity;
 }> => {
   const installationPaths = (await host.installationPaths?.()) ?? [];
-  const registrations = (await host.clientRegistrations?.(scope.clients)) ?? [];
+  const registrations =
+    (await host.clientRegistrations?.(
+      scope.clients,
+      Object.fromEntries(
+        selections.flatMap(({ settings }) => Object.entries(settings)),
+      ),
+    )) ?? [];
   const skillClientIds =
     scope.skill_clients ??
     (scope.clients.length > 0 ? scope.clients : undefined);
@@ -786,12 +874,20 @@ export const systemDoctorHost = (
         throw failure;
       }
     },
-    clientRegistrations: (selectedClientIds) =>
+    clientRegistrations: (selectedClientIds, providerSettings) =>
       readClientRegistrationStatuses(homeDirectory, undefined, {
         platform,
         environment,
         resources,
         ...(selectedClientIds === undefined ? {} : { selectedClientIds }),
+        ...(providerSettings === undefined
+          ? {}
+          : {
+              providerSettings: registrationSpelledSettings(
+                providerSettings,
+                environment,
+              ),
+            }),
         ...(resolveProviderRequestBudget === undefined
           ? {}
           : {

src/application/DoctorRegistrationEnvironment.test.ts

@@ -0,0 +1,184 @@
+import { writeFile } from "node:fs/promises";
+import { join } from "node:path";
+import { expect, it } from "vitest";
+
+import { createTestTempDirectory } from "../../tests/fixtures/temporaryDirectory.js";
+import { createDoctorHostFixture as host } from "./Doctor.fixture.js";
+import { runDoctor, systemDoctorHost, type DoctorHost } from "./Doctor.js";
+
+const inspection = (
+  id: string,
+  registrationEnvironment: Readonly<Record<string, string>>,
+  available = true,
+) => ({
+  id,
+  configured: true,
+  available,
+  providerVersion: null,
+  registrationEnvironment,
+  checks: [],
+});
+const recordingHost = (overrides: Partial<DoctorHost>) => {
+  const requested: Readonly<Record<string, string>>[] = [];
+  return {
+    requested,
+    host: host({
+      clientRegistrations: (_clients, providerSettings) => {
+        requested.push(providerSettings ?? {});
+        return Promise.resolve([
+          {
+            client: "cursor",
+            config_path: "/home/user/.cursor/mcp.json",
+            command: ["/current/rea", "mcp"],
+            state: "aligned",
+            remediation: null,
+            provider_settings: {
+              unrecorded: ["GHIDRA_INSTALL_DIR"],
+              differing: [],
+              unresolved: [],
+            },
+          },
+        ]);
+      },
+      ...overrides,
+    }),
+  };
+};
+const selectedProviders = {
+  providerInspections: () =>
+    Promise.resolve([
+      inspection("ghidra", { GHIDRA_INSTALL_DIR: "/opt/ghidra" }),
+      inspection("jadx", { REA_JADX_MCP_JAR: "/opt/jadx.jar" }),
+      inspection("kuna", { REA_KUNA_COMMAND: "/opt/kuna" }, false),
+    ]),
+};
+const CHECK = "registration_environment:cursor";
+
+it("compares only settings an available provider relied on", async () => {
+  const { host: selectedHost, requested } = recordingHost(selectedProviders);
+  await runDoctor(undefined, selectedHost);
+  expect(requested).toEqual([
+    {
+      GHIDRA_INSTALL_DIR: "/opt/ghidra",
+      REA_JADX_MCP_JAR: "/opt/jadx.jar",
+    },
+  ]);
+});
+
+it.each([
+  [{ providers: ["ghidra"] }, true],
+  [{ clients: ["cursor"] }, true],
+  [{ clients: ["codex"] }, false],
+  [{ providers: ["jadx"] }, false],
+  [{ skill: true }, false],
+])("follows the selected scope %j", async (scope, selected) => {
+  const report = await runDoctor(
+    undefined,
+    recordingHost(selectedProviders).host,
+    scope,
+  );
+  const inScope = report.scope_checks.some(({ name }) => name === CHECK);
+  expect(inScope).toBe(selected);
+  expect(report.informational_checks.some(({ name }) => name === CHECK)).toBe(
+    !selected,
+  );
+});
+
+it("does not gate health or name unaffected providers", async () => {
+  const report = await runDoctor(
+    undefined,
+    recordingHost(selectedProviders).host,
+    { providers: ["ghidra"] },
+  );
+  expect(report.healthy).toBe(true);
+  expect(report.checks).toContainEqual(
+    expect.objectContaining({
+      name: CHECK,
+      ok: true,
+      classification: "unknown",
+      details: { effective_environment: "unknown", providers: ["ghidra"] },
+    }),
+  );
+});
+
+it.each([
+  ["/custom/Hopper", { HOPPER_LAUNCHER_PATH: "/custom/Hopper" }],
+  // A default location is found again without this terminal's environment.
+  [undefined, {}],
+])(
+  "includes Hopper only for an explicit available path (%s)",
+  async (configuredHopperPath, expected) => {
+    const { host: selectedHost, requested } = recordingHost(
+      configuredHopperPath === undefined ? {} : { configuredHopperPath },
+    );
+    await runDoctor(undefined, selectedHost);
+    expect(requested).toEqual([expected]);
+  },
+);
+
+it("does not include an explicit Hopper path that fails its checks", async () => {
+  const { host: selectedHost, requested } = recordingHost({
+    configuredHopperPath: "/custom/missing",
+    executable: () => Promise.resolve(false),
+  });
+  await runDoctor(undefined, selectedHost);
+  expect(requested).toEqual([{}]);
+});
+
+it("compares a caller selection as setup spells it", async () => {
+  const home = await createTestTempDirectory("rea-doctor-spelling-");
+  await writeFile(
+    join(home, ".claude.json"),
+    JSON.stringify({
+      mcpServers: {
+        rea: {
+          command: "/current/rea",
+          args: ["mcp"],
+          env: {
+            GHIDRA_INSTALL_DIR: "/opt/ghidra",
+            JAVA_HOME: "/selected/alias",
+          },
+        },
+      },
+    }),
+  );
+  const system = systemDoctorHost({
+    environment: { HOME: home, JAVA_HOME: "/selected/alias" },
+  });
+  const statuses = await system.clientRegistrations?.(["claude_code"], {
+    GHIDRA_INSTALL_DIR: "/opt/ghidra",
+    // The provider's observed home; setup records the caller's spelling.
+    JAVA_HOME: "/observed/jdk",
+  });
+  await system.close?.();
+  expect(statuses?.[0]?.client).toBe("claude_code");
+  expect(statuses?.[0]).not.toHaveProperty("provider_settings");
+});
+
+it("states each comparison result without a claim it did not establish", async () => {
+  const report = await runDoctor(
+    undefined,
+    host({
+      clientRegistrations: () =>
+        Promise.resolve([
+          {
+            client: "cursor",
+            config_path: "/cursor.json",
+            command: ["/current/rea", "mcp"],
+            state: "aligned",
+            remediation: null,
+            provider_settings: {
+              unrecorded: [],
+              differing: ["JAVA_HOME"],
+              unresolved: ["GHIDRA_INSTALL_DIR"],
+            },
+          },
+        ]),
+    }),
+  );
+  const detail = report.checks.find(({ name }) => name === CHECK)?.detail;
+  expect(detail).toContain("what the server cursor starts receives is unknown");
+  expect(detail).toContain("records other values for JAVA_HOME");
+  expect(detail).toContain("could not resolve its GHIDRA_INSTALL_DIR");
+  expect(detail).not.toContain("does not record");
+});

src/application/DoctorScope.ts

@@ -72,6 +72,9 @@ export const scopeDoctorChecks = (
       input.registrations.find((candidate) => candidate.client === client),
     ),
   );
+  const environmentChecks = input.checks.filter((check) =>
+    registrationEnvironmentInScope(check, input.scope),
+  );
   const skillChecks = input.scope.skill
     ? [selectedSkillCheck(input.skillState, input.checks)]
     : [];
@@ -111,6 +114,7 @@ export const scopeDoctorChecks = (
     ...hopperHostChecks,
     ...selectedProviderChecks,
     ...clientChecks,
+    ...environmentChecks,
     ...skillChecks,
   ];
   const selectedNames = new Set(scopeChecks.map(({ name }) => name));
@@ -129,6 +133,22 @@ export const scopeDoctorChecks = (
   };
 };
 
+/** Follow the caller's question: a named client, or a provider it relies on. */
+const registrationEnvironmentInScope = (
+  { name, details }: DoctorCheck,
+  scope: DoctorScopeReport,
+): boolean => {
+  const [family, client] = name.split(":");
+  if (family !== "registration_environment" || client === undefined)
+    return false;
+  const providers = details?.providers;
+  return (
+    scope.clients.includes(client) ||
+    (Array.isArray(providers) &&
+      scope.providers.some((provider) => providers.includes(provider)))
+  );
+};
+
 const isProviderCheck = (
   name: string,
   inspections: readonly DoctorProviderInspection[] | undefined,

src/application/EnhancedToolTypes.ts

@@ -3,7 +3,7 @@ import type { z } from "zod";
 import { analysisInputErrorFromIssues } from "../domain/inputIssueProjection.js";
 import type { AnalysisError } from "../domain/analysisErrorBase.js";
 import type { JsonValue } from "../domain/jsonValue.js";
-import type { TraceContainingProcedure } from "../domain/native/nativeObservation.js";
+import type { LiteralFeatureReference } from "../domain/native/literalFeatureTrace.js";
 import { err, type Result } from "../domain/result.js";
 import {
   enhancedInputSchemas,
@@ -27,11 +27,7 @@ export const failedWithPartialResult = (
   error: AnalysisError,
   partialResult: JsonValue,
 ): PartialEnhancedFailure => ({ ok: false, error, partialResult });
-export type TraceReference = {
-  readonly target_address: string;
-  readonly source_address: string;
-  readonly containing_procedure: TraceContainingProcedure;
-};
+export type TraceReference = LiteralFeatureReference;
 
 /** One enhanced call whose input was parsed at its owning adapter boundary. */
 export type ValidatedEnhancedCall = {

src/application/EvidenceBundleCommands.ts

@@ -297,10 +297,12 @@ const projectWrite = (
 export const inspectEvidenceBundleCommand = async (
   input: {
     readonly path: string;
-    readonly detail: "complete" | "summary" | "records";
+    readonly detail: "complete" | "summary" | "records" | "links";
     readonly filters?: EvidenceRecordFilters | undefined;
     readonly offset?: number | undefined;
     readonly limit?: number | undefined;
+    readonly traversal?: "direct" | "retained-closure" | undefined;
+    readonly link_status?: "missing" | "retained" | "all" | undefined;
   },
   signal?: AbortSignal,
 ) => {

src/application/ReferenceSourceImportTypes.ts

@@ -125,6 +125,8 @@ export interface ReferenceSourceImportOptions {
 export const DEFAULT_REFERENCE_SOURCE_IGNORE_PATTERNS = [
   ".git/",
   ".git/hooks/",
+  // Match pointer files after directory rules to preserve their provenance.
+  ".git",
   "node_modules/",
   "dist/",
   "build/",

src/application/Setup.planning.test.ts

@@ -301,10 +301,13 @@ describe("setup client selection", () => {
       configPath: "/codex.toml",
       format: "toml" as const,
     };
-    host.clients = [codex];
+    host.clients = [
+      codex,
+      { name: "grok_bot", configPath: "/grokbot", format: "unsupported" },
+    ];
     host.availableClients = [
       { name: "cursor", configPath: "/cursor.json" },
-      codex,
+      ...host.clients,
     ];
 
     const result = await runSetup(
@@ -331,6 +334,31 @@ describe("setup client selection", () => {
     expect(host.skillInstalls).toBe(0);
   });
 
+  it.each([undefined, false])(
+    "omits manual clients from automatic readiness while preserving detection (skill: %s)",
+    async (installSkill) => {
+      const host = new FakeSetupHost();
+      host.clients = [
+        { name: "grok_bot", configPath: "/grokbot", format: "unsupported" },
+      ];
+      const result = await runSetup(
+        {
+          ...options(true),
+          allDetectedClients: true,
+          ...(installSkill === undefined ? {} : { installSkill }),
+        },
+        host,
+      );
+      expect(result.status).toBe("ready");
+      expect(result.doctor.scope.clients).toEqual([]);
+      expect(result.clientStates).toMatchObject([
+        { client: { name: "grok_bot" }, detected: true },
+      ]);
+      expect(result.clients).toEqual({});
+      expect(host.configurations).toBe(0);
+    },
+  );
+
   it.each([true, false])(
     "handles repeated clients once in first-selected order (dry run: %s)",
     async (dryRun) => {

src/application/SetupPlan.ts

@@ -139,7 +139,9 @@ export const discoverSetupState = async (input: {
     installHopper,
     hopperInstall,
     clients,
-    detectedClientIds: [...detectedIds],
+    detectedClientIds: detectedClients
+      .filter(({ format }) => format !== "unsupported")
+      .map(({ name }) => name),
     defaultClientIds,
     clientStates,
     ...(linuxDistribution?.packageFamily === undefined

src/application/SetupRegistrationEnvironment.ts

@@ -107,3 +107,17 @@ export const providerRegistrationEnvironment = (
       )
       .sort(([left], [right]) => compareUnicodeCodePoints(left, right)),
   );
+
+/** Spell selected settings as setup records them: an explicit selection wins. */
+export const registrationSpelledSettings = (
+  settings: Readonly<Record<string, string>>,
+  environment: Readonly<Record<string, string | undefined>>,
+): Readonly<Record<string, string>> => {
+  const explicit = explicitSetupRegistrationEnvironment(environment);
+  return Object.fromEntries(
+    Object.entries(settings).map(([key, value]) => [
+      key,
+      explicit[key] ?? value,
+    ]),
+  );
+};

src/application/analysisView/NativeObservationViews.test.ts

@@ -121,53 +121,56 @@ const graph = (): NativeCallGraph =>
     limitations: ["Graph caveat", "Graph caveat"],
   });
 
-it("returns useful caller/callee facts with exact source context identity and partial coverage", async () => {
-  const source = parent("procedure_callees", [
-    "ram:0x0010",
-    "ram:0x0010",
-    "ram:0x0020",
-  ]);
-  const before = JSON.stringify(source);
-  const summary = await project(source, { kind: "summary" });
-  expect(summary.value).toMatchObject({
-    kind: "summary",
-    parent_evidence_id: source.evidence_id,
-    source_provider: source.provider,
-    source_parameters: source.parameters,
-    source_analysis_profile_digest: source.analysis_profile?.digest,
-    source_context: {
-      evidence_limitation_count: 1,
-      result_limitation_count: null,
-    },
-    summary: { observations: 3 },
-    items: {
-      type: "addresses",
-      rows: [
-        { source_index: 0, address: "ram:0x0010" },
-        { source_index: 1, address: "ram:0x0010" },
-        { source_index: 2, address: "ram:0x0020" },
-      ],
-    },
-  });
-  expect(summary.evidence.relationship_coverage).toEqual(
-    source.relationship_coverage,
-  );
-  const page = await project(source, {
-    kind: "native-observation",
-    offset: 1,
-    limit: 1,
-  });
-  expect(page.value).toMatchObject({
-    items: { rows: [{ source_index: 1, address: "ram:0x0010" }] },
-    coverage: { total: 3, next_offset: 2, exhausted: false },
-  });
-  expect(page.value).toHaveProperty(
-    "source_context.digest",
-    contextDigest(summary.value),
-  );
-  expect(JSON.stringify(summary.value)).not.toContain('"analysis_profile":');
-  expect(JSON.stringify(source)).toBe(before);
-});
+it.each(["procedure_callees", "xrefs"])(
+  "pages %s addresses with exact source context and duplicate identity",
+  async (operation) => {
+    const source = parent(operation, [
+      "ram:0x0010",
+      "ram:0x0010",
+      "ram:0x0020",
+    ]);
+    const before = JSON.stringify(source);
+    const summary = await project(source, { kind: "summary" });
+    expect(summary.value).toMatchObject({
+      kind: "summary",
+      parent_evidence_id: source.evidence_id,
+      source_provider: source.provider,
+      source_parameters: source.parameters,
+      source_analysis_profile_digest: source.analysis_profile?.digest,
+      source_context: {
+        evidence_limitation_count: 1,
+        result_limitation_count: null,
+      },
+      summary: { observations: 3 },
+      items: {
+        type: "addresses",
+        rows: [
+          { source_index: 0, address: "ram:0x0010" },
+          { source_index: 1, address: "ram:0x0010" },
+          { source_index: 2, address: "ram:0x0020" },
+        ],
+      },
+    });
+    expect(summary.evidence.relationship_coverage).toEqual(
+      source.relationship_coverage,
+    );
+    const page = await project(source, {
+      kind: "native-observation",
+      offset: 1,
+      limit: 1,
+    });
+    expect(page.value).toMatchObject({
+      items: { rows: [{ source_index: 1, address: "ram:0x0010" }] },
+      coverage: { total: 3, next_offset: 2, exhausted: false },
+    });
+    expect(page.value).toHaveProperty(
+      "source_context.digest",
+      contextDigest(summary.value),
+    );
+    expect(JSON.stringify(summary.value)).not.toContain('"analysis_profile":');
+    expect(JSON.stringify(source)).toBe(before);
+  },
+);
 
 it("pages complete context fields and changes its digest when source profile or caveats change", async () => {
   const source = parent("procedure_callers", []);

src/application/binary/AnalysisSnapshotCache.test.ts

@@ -7,7 +7,8 @@ import {
   ANALYSIS_SNAPSHOT_PROVIDER,
   ANALYSIS_SNAPSHOT_TARGET,
 } from "../../domain/analysisSnapshot.fixture.js";
-import { createEvidence } from "../../domain/evidence.js";
+import { createEvidence, immutableEvidence } from "../../domain/evidence.js";
+import { createAnalysisExecutionEvidence } from "../../domain/analysisObservation.js";
 import {
   createEvidenceBundle,
   evidenceBundleForTarget,
@@ -1208,6 +1209,154 @@ it("declines source-bearing snapshot entries while replaying omitted and empty s
   expect(cache.entries()).toHaveLength(2);
 });
 
+it("replays source-bearing entries only when their complete retained closure exists", () => {
+  const target = ANALYSIS_SNAPSHOT_TARGET;
+  const profile = ANALYSIS_SNAPSHOT_PROFILE;
+  const leaf = immutableEvidence(
+    createEvidence(target, ANALYSIS_SNAPSHOT_PROVIDER, {
+      operation: "leaf",
+      parameters: {},
+      result: "leaf observation",
+    }),
+  );
+  const source = immutableEvidence(
+    createEvidence(target, ANALYSIS_SNAPSHOT_PROVIDER, {
+      operation: "source",
+      parameters: {},
+      result: "source observation",
+      evidenceLinks: [leaf.evidence_id],
+    }),
+  );
+  const parameters = { address: "0x1000", document: "fixture" };
+  const execution = createAnalysisExecution(
+    "parent observation",
+    ANALYSIS_SNAPSHOT_PROVIDER,
+    {
+      subject: target,
+      analysisProfile: profile,
+      sourceEvidence: [source],
+    },
+  );
+  const parent = immutableEvidence(
+    createAnalysisExecutionEvidence(
+      "procedure_info",
+      parameters,
+      execution,
+      "observed",
+    ),
+  );
+  const complete = new Map(
+    [parent, source, leaf].map((record) => [record.evidence_id, record]),
+  );
+  const input = {
+    target,
+    profile,
+    operation: "procedure_info" as const,
+    parameters,
+    execution: { ...execution, evidenceId: parent.evidence_id },
+  };
+  const missingLeaf = new AnalysisSnapshotCache();
+  missingLeaf.record(input, (id) =>
+    id === leaf.evidence_id ? undefined : complete.get(id),
+  );
+  expect(
+    missingLeaf.lookup(target, profile, "procedure_info", parameters),
+  ).toBeUndefined();
+  const cache = new AnalysisSnapshotCache();
+  cache.record(input, (id) => complete.get(id));
+  expect(
+    cache
+      .lookup(target, profile, "procedure_info", parameters)
+      ?.sourceEvidence?.map((record) => record.evidence_id),
+  ).toEqual([source.evidence_id]);
+  if (source.subject === null) throw new Error("Expected source subject");
+  const ledger = new EvidenceLedger();
+  for (const record of [parent, source, leaf])
+    expect(ledger.record(record).ok).toBe(true);
+  const movedSource = {
+    ...source,
+    subject: {
+      ...source.subject,
+      local_path: "/relocated/source",
+      name: "source",
+    },
+  };
+  const replacement = ledger.import(createEvidenceBundle([movedSource]));
+  if (!replacement.ok) throw replacement.error;
+  cache.refreshEvidenceMetadata(replacement.value.replacements);
+  expect(
+    cache.lookup(target, profile, "procedure_info", parameters)
+      ?.sourceEvidence?.[0]?.subject?.local_path,
+  ).toBe("/relocated/source");
+  const exported = cache.export(target, profile, ledger.export());
+  if (!exported.ok) throw exported.error;
+  const imported = new AnalysisSnapshotCache();
+  imported.stage(exported.value);
+  expect(
+    imported
+      .lookup(target, profile, "procedure_info", parameters)
+      ?.sourceEvidence?.map((record) => record.evidence_id),
+  ).toEqual([source.evidence_id]);
+  expect(
+    imported.lookup(target, profile, "procedure_info", parameters)
+      ?.sourceEvidence?.[0]?.subject?.local_path,
+  ).toBe("/relocated/source");
+  const pruned = parseAnalysisSnapshot({
+    ...exported.value,
+    evidence_bundle: createEvidenceBundle([parent, movedSource]),
+  });
+  const incomplete = new AnalysisSnapshotCache();
+  incomplete.stage(pruned);
+  const partial = new Map(
+    [parent, movedSource].map((record) => [record.evidence_id, record]),
+  );
+  expect(
+    incomplete.lookup(target, profile, "procedure_info", parameters, (id) =>
+      partial.get(id),
+    ),
+  ).toBeUndefined();
+  partial.set(leaf.evidence_id, leaf);
+  expect(
+    incomplete
+      .lookup(target, profile, "procedure_info", parameters, (id) =>
+        partial.get(id),
+      )
+      ?.sourceEvidence?.map((record) => record.evidence_id),
+  ).toEqual([source.evidence_id]);
+
+  const otherSource = immutableEvidence(
+    createEvidence(target, ANALYSIS_SNAPSHOT_PROVIDER, {
+      operation: "other_source",
+      parameters: {},
+      result: "different source",
+    }),
+  );
+  const otherParent = immutableEvidence(
+    createAnalysisExecutionEvidence(
+      "procedure_info",
+      parameters,
+      { ...execution, sourceEvidence: [otherSource] },
+      "observed",
+    ),
+  );
+  const records = [parent, movedSource, leaf, otherParent, otherSource];
+  const ambiguous = new AnalysisSnapshotCache();
+  ambiguous.stage(
+    parseAnalysisSnapshot({
+      ...exported.value,
+      evidence_bundle: createEvidenceBundle(records),
+    }),
+  );
+  const allRecords = new Map(
+    records.map((record) => [record.evidence_id, record]),
+  );
+  expect(
+    ambiguous.lookup(target, profile, "procedure_info", parameters, (id) =>
+      allRecords.get(id),
+    ),
+  ).toBeUndefined();
+});
+
 describe("executions that report truncated references", () => {
   const record = (referencesTruncated: boolean | undefined) => {
     const cache = new AnalysisSnapshotCache();

src/application/binary/AnalysisSnapshotCache.ts

@@ -45,6 +45,7 @@ import {
   snapshotReplayBinding,
   type SnapshotReplayBinding,
 } from "./AnalysisSnapshotReplayBinding.js";
+import { createInvestigationEvidenceClosureChecker } from "../investigation/InvestigationEvidence.js";
 
 const RELATIONSHIP_OPERATIONS: ReadonlySet<AnalysisOperation> = new Set([
   "procedure_callers",
@@ -147,9 +148,12 @@ export const SNAPSHOT_REPLAY_LIMITATION =
 /** Bounded in-memory cache for one immutable binary identity. */
 export class AnalysisSnapshotCache {
   readonly #entries = new Map<string, AnalysisSnapshotEntry>();
-  // Null means imported provenance cannot be faithfully replayed. It is distinct
-  // from an entry recorded before an Evidence ID was assigned.
-  readonly #replayBindings = new Map<string, SnapshotReplayBinding | null>();
+  // Null is ambiguous provenance; a pending ID is an exact parent whose source
+  // closure was missing and can be checked again against the owning ledger.
+  readonly #replayBindings = new Map<
+    string,
+    SnapshotReplayBinding | { readonly pendingEvidenceId: string } | null
+  >();
   readonly #workflowEntries = new Map<string, AnalysisSnapshotWorkflowEntry>();
   #target: AnalysisSnapshotTarget | undefined;
   #binding: AnalysisSnapshotBinding | undefined;
@@ -218,6 +222,10 @@ export class AnalysisSnapshotCache {
         record,
       ]),
     );
+    const lookup = (id: string) => records.get(id);
+    const checkClosure = createInvestigationEvidenceClosureChecker({
+      evidenceForAnalysis: lookup,
+    });
     const ambiguous = new Set<string>();
     for (const evidence of snapshot.evidence_bundle.records) {
       const queryId = analysisQueryId(
@@ -242,11 +250,15 @@ export class AnalysisSnapshotCache {
       else evidenceByQuery.set(queryId, evidence);
     }
     for (const [queryId, evidence] of evidenceByQuery) {
+      if (ambiguous.has(queryId)) {
+        this.#replayBindings.set(queryId, null);
+        continue;
+      }
       this.#replayBindings.set(
         queryId,
-        ambiguous.has(queryId)
-          ? null
-          : snapshotReplayBinding(evidence, records),
+        snapshotReplayBinding(evidence, lookup, checkClosure) ?? {
+          pendingEvidenceId: evidence.evidence_id,
+        },
       );
     }
     for (const entry of snapshot.workflow_entries) {
@@ -272,7 +284,12 @@ export class AnalysisSnapshotCache {
       replacements.map(({ current }) => [current.evidence_id, current]),
     );
     for (const [queryId, binding] of this.#replayBindings) {
-      if (binding === null || binding.sourceEvidence === undefined) continue;
+      if (
+        binding === null ||
+        "pendingEvidenceId" in binding ||
+        binding.sourceEvidence === undefined
+      )
+        continue;
       const sources = binding.sourceEvidence;
       if (!sources.some((source) => currentRecords.has(source.evidence_id)))
         continue;
@@ -475,6 +492,7 @@ export class AnalysisSnapshotCache {
     profile: AnalysisProfileCommitment,
     operation: AnalysisOperation,
     parameters: Readonly<Record<string, JsonValue>>,
+    lookup?: (id: string) => Evidence | undefined,
   ): AnalysisExecution | undefined {
     const queryId = analysisQueryId(
       snapshotTarget(target),
@@ -484,10 +502,18 @@ export class AnalysisSnapshotCache {
     );
     const cached = this.#entries.get(queryId);
     if (cached === undefined) return undefined;
-    const binding = this.#replayBindings.get(queryId);
+    let binding = this.#replayBindings.get(queryId);
     // Do not turn a refused provenance selection into a fresh, unlinked record.
     // The provider must produce a new observation before this query can replay.
     if (binding === null) return undefined;
+    if (binding !== undefined && "pendingEvidenceId" in binding) {
+      const parent = lookup?.(binding.pendingEvidenceId);
+      if (parent === undefined || lookup === undefined) return undefined;
+      const restored = snapshotReplayBinding(parent, lookup);
+      if (restored === null) return undefined;
+      this.#replayBindings.set(queryId, restored);
+      binding = restored;
+    }
     const cachedSubject = cached.execution.subject;
     const subject =
       cachedSubject == null
@@ -535,21 +561,30 @@ export class AnalysisSnapshotCache {
   }
 
   /** Record one successful immutable call unless the cache is full. */
-  record(input: {
-    readonly target: BinaryTarget;
-    readonly profile: AnalysisProfileCommitment;
-    readonly operation: AnalysisOperation;
-    readonly parameters: Readonly<Record<string, JsonValue>>;
-    readonly execution: AnalysisExecution;
-  }): void {
+  record(
+    input: {
+      readonly target: BinaryTarget;
+      readonly profile: AnalysisProfileCommitment;
+      readonly operation: AnalysisOperation;
+      readonly parameters: Readonly<Record<string, JsonValue>>;
+      readonly execution: AnalysisExecution;
+    },
+    lookup?: (id: string) => Evidence | undefined,
+  ): void {
     const { target, profile, operation, parameters, execution } = input;
     this.select(target, profile);
     // The snapshot format does not carry reference truncation; a replay would
     // present a capped read as complete, so it is not recorded.
     if (execution.referencesTruncated === true) return;
-    // Provider snapshot entries do not carry execution source records. Replay
-    // must not discard the source closure that supplies the parent's Evidence links.
-    if ((execution.sourceEvidence?.length ?? 0) > 0) return;
+    let sourceBinding: SnapshotReplayBinding | undefined;
+    if ((execution.sourceEvidence?.length ?? 0) > 0) {
+      if (execution.evidenceId === undefined || lookup === undefined) return;
+      const parent = lookup(execution.evidenceId);
+      if (parent === undefined) return;
+      const closed = snapshotReplayBinding(parent, lookup);
+      if (closed === null) return;
+      sourceBinding = closed;
+    }
     const queryId = analysisQueryId(
       snapshotTarget(target),
       snapshotBinding(profile),
@@ -581,9 +616,10 @@ export class AnalysisSnapshotCache {
     if (execution.evidenceId === undefined)
       this.#replayBindings.delete(entry.query_id);
     else
-      this.#replayBindings.set(entry.query_id, {
-        evidenceId: execution.evidenceId,
-      });
+      this.#replayBindings.set(
+        entry.query_id,
+        sourceBinding ?? { evidenceId: execution.evidenceId },
+      );
   }
 
   /** Forget all target-bound entries. */

src/application/binary/AnalysisSnapshotReplayBinding.ts

@@ -1,4 +1,5 @@
 import type { Evidence } from "../../domain/evidence.js";
+import { createInvestigationEvidenceClosureChecker } from "../investigation/InvestigationEvidence.js";
 
 /** Authenticated observation identity and its immediate source records. */
 export interface SnapshotReplayBinding {
@@ -9,13 +10,17 @@ export interface SnapshotReplayBinding {
 /** Preserve direct links using the snapshot's authenticated immutable records. */
 export const snapshotReplayBinding = (
   evidence: Evidence,
-  records: ReadonlyMap<string, Evidence>,
+  lookup: (id: string) => Evidence | undefined,
+  checkClosure = createInvestigationEvidenceClosureChecker({
+    evidenceForAnalysis: lookup,
+  }),
 ): SnapshotReplayBinding | null => {
   if (evidence.evidence_links.length === 0)
     return { evidenceId: evidence.evidence_id };
+  if (!checkClosure(evidence.evidence_links)) return null;
   const sources: Evidence[] = [];
   for (const id of evidence.evidence_links) {
-    const source = records.get(id);
+    const source = lookup(id);
     // An external link without its source cannot be represented by sourceEvidence.
     if (source === undefined) return null;
     sources.push(source);

src/application/binary/BinarySessionRecords.ts

@@ -323,14 +323,16 @@ export abstract class BinarySessionRecords {
     >,
   ): AnalysisExecution | undefined {
     if (this.#snapshotInvalidated) return undefined;
-    return this.#snapshot.lookup(target, profile, operation, parameters);
+    return this.#snapshot.lookup(target, profile, operation, parameters, (id) =>
+      this.evidenceForAnalysis(id),
+    );
   }
 
   protected recordSnapshot(
     input: Parameters<AnalysisSnapshotCache["record"]>[0],
   ): void {
     if (this.#snapshotInvalidated) return;
-    this.#snapshot.record(input);
+    this.#snapshot.record(input, (id) => this.evidenceForAnalysis(id));
     this.#emitSnapshotChanged();
   }
 

src/application/binaryDiagnostics/BinaryLayoutService.test.ts

@@ -58,6 +58,7 @@ it("records the decoded layout once in its Evidence", async () => {
 
 it.each([
   [{ machine: "EM_X86_64", bits: 64, byte_order: "little" }, "x86_64"],
+  [{ machine: "EM_AARCH64", bits: 64, byte_order: "little" }, "arm64"],
   [{ machine: "EM_386", bits: 32, byte_order: "little" }, "x86"],
   [{ machine: "EM_ARM", bits: 32, byte_order: "little" }, "arm"],
   [{ machine: "EM_MIPS", bits: 32, byte_order: "big" }, "mips"],

src/application/binaryDiagnostics/BinaryLayoutService.ts

@@ -14,6 +14,7 @@ import { parseAnalysisInput } from "../AnalysisInput.js";
 const OPERATION = "inspect_binary_layout";
 const EVIDENCE_ARCHITECTURES = {
   EM_X86_64: "x86_64",
+  EM_AARCH64: "arm64",
   EM_386: "x86",
   EM_ARM: "arm",
   EM_MIPS: "mips",

src/application/environment/environmentCompare.test.ts

@@ -64,6 +64,56 @@ const compare = (...probes: (readonly TimedCaptureRow[])[]) => {
   return report.value;
 };
 
+describe("step difference coverage", () => {
+  it("keeps categories from differences beyond the returned prefix", () => {
+    const fields = Object.fromEntries(
+      Array.from({ length: 20 }, (_, index) => [`field${String(index)}`, 0]),
+    );
+    const capture = timedCaptureEvidence([["GET", "/api/config", fields]]);
+    const served = environmentStateServeFixture(capture);
+    const report = compareEnvironment({
+      source: environmentServeSource(served),
+      captureValue: capture,
+      probes: [
+        {
+          label: "changed",
+          value: timedCaptureEvidence([
+            [
+              "GET",
+              "/api/config",
+              {
+                ...Object.fromEntries(
+                  Object.keys(fields).map((key) => [key, 1]),
+                ),
+                z_missing: true,
+              },
+            ],
+          ]),
+        },
+      ],
+      operation: "environment-compare",
+    });
+    if (!report.ok) throw report.error;
+    const step = report.value.probes[0]!.results[0]!;
+    expect(step).toMatchObject({
+      equal: false,
+      equal_ignoring_order: false,
+      categories: ["value", "missing-field"],
+      differences_total: 21,
+      differences_omitted: 1,
+      differences_truncated: true,
+    });
+    expect(step.differences).toHaveLength(20);
+    expect(step.differences.every(({ category }) => category === "value")).toBe(
+      true,
+    );
+    expect(report.value.summary.categories).toMatchObject({
+      value: 1,
+      "missing-field": 1,
+    });
+  });
+});
+
 describe("matchProbeRequest", () => {
   it("compares a repeated-query probe against the matching recorded response", () => {
     const recorded = timedCaptureEvidence([

src/application/environment/environmentCompare.ts

@@ -81,6 +81,10 @@ export interface CompareStep {
   readonly equal_ignoring_order: boolean;
   readonly categories: DifferenceCategory[];
   readonly differences: Difference[];
+  /** All differences computed for this step, before the returned list is capped. */
+  readonly differences_total: number;
+  readonly differences_omitted: number;
+  readonly differences_truncated: boolean;
   readonly ignored_query: string[];
 }
 
@@ -287,6 +291,8 @@ const stepOf = (
   outcome: { env_status: number | null; differences: Difference[] },
 ): CompareStep => {
   const categories = [...new Set(outcome.differences.map((d) => d.category))];
+  const differences = outcome.differences.slice(0, STEP_DIFFERENCE_LIMIT);
+  const omitted = outcome.differences.length - differences.length;
   return {
     ...base,
     tool: call?.tool.name ?? null,
@@ -296,7 +302,10 @@ const stepOf = (
       (difference) => difference.category === "order",
     ),
     categories,
-    differences: outcome.differences.slice(0, STEP_DIFFERENCE_LIMIT),
+    differences,
+    differences_total: outcome.differences.length,
+    differences_omitted: omitted,
+    differences_truncated: omitted > 0,
     ignored_query: [...(call?.ignoredQuery ?? [])],
   };
 };

src/application/investigation/InspectEvidenceBundle.ts

@@ -2,24 +2,41 @@ import type { EvidenceBundle } from "../../domain/evidenceBundle.js";
 import { AnalysisInputError } from "../../domain/analysisErrorCore.js";
 import { err, ok, type Result } from "../../domain/result.js";
 import {
+  inspectEvidenceLinks,
   selectEvidenceRecords,
   summarizeEvidenceBundle,
   type EvidenceBundleSummary,
+  type EvidenceLinkInspection,
   type EvidenceRecordFilters,
   type EvidenceRecordSelection,
 } from "../../domain/evidenceRecordSummary.js";
 
-/** Select complete bundle delivery, discovery metadata, or a page of complete selected records. */
+type InspectionDetail = "complete" | "summary" | "records" | "links";
+
+/** Fields owned by particular deliveries, refused elsewhere rather than ignored. */
+const DELIVERY_FIELDS = [
+  ["offset", ["records", "links"]],
+  ["limit", ["records", "links"]],
+  ["traversal", ["links"]],
+  ["link_status", ["links"]],
+] as const;
+
+/** Select complete delivery, discovery metadata, complete records, or link membership. */
 export const inspectEvidenceBundle = (
   bundle: EvidenceBundle,
   options: {
-    readonly detail: "complete" | "summary" | "records";
+    readonly detail: InspectionDetail;
     readonly filters?: EvidenceRecordFilters | undefined;
     readonly offset?: number | undefined;
     readonly limit?: number | undefined;
+    readonly traversal?: "direct" | "retained-closure" | undefined;
+    readonly link_status?: "missing" | "retained" | "all" | undefined;
   },
 ): Result<
-  EvidenceBundle | EvidenceBundleSummary | EvidenceRecordSelection,
+  | EvidenceBundle
+  | EvidenceBundleSummary
+  | EvidenceRecordSelection
+  | EvidenceLinkInspection,
   AnalysisInputError
 > => {
   if (options.detail === "complete" && options.filters !== undefined)
@@ -29,29 +46,34 @@ export const inspectEvidenceBundle = (
           path: ["filters"],
           reason: "invalid_value",
           message:
-            "Record filters require detail: summary or records; complete returns the canonical bundle.",
-          expected: "detail: summary or records",
+            "Record filters require detail: summary, records or links; complete returns the canonical bundle.",
+          expected: "detail: summary, records or links",
         },
       ]),
     );
-  if (options.detail !== "records") {
-    const paging = (["offset", "limit"] as const).filter(
-      (field) => options[field] !== undefined,
-    );
-    if (paging.length > 0)
-      return err(
-        new AnalysisInputError(
-          "get_evidence_bundle",
-          undefined,
-          paging.map((field) => ({
+  const misplaced = DELIVERY_FIELDS.filter(
+    ([field, details]) =>
+      options[field] !== undefined &&
+      !(details as readonly InspectionDetail[]).includes(options.detail),
+  );
+  if (misplaced.length > 0)
+    return err(
+      new AnalysisInputError(
+        "get_evidence_bundle",
+        undefined,
+        misplaced.map(([field, details]) => {
+          const expected = details
+            .map((detail) => `detail: ${detail}`)
+            .join(" or ");
+          return {
             path: [field],
             reason: "invalid_value" as const,
-            message: `${field} pages complete records and requires detail: records.`,
-            expected: "detail: records",
-          })),
-        ),
-      );
-  }
+            message: `${field} requires ${expected}.`,
+            expected,
+          };
+        }),
+      ),
+    );
   if (options.detail === "records")
     return ok(
       selectEvidenceRecords(bundle, options.filters, {
@@ -59,6 +81,15 @@ export const inspectEvidenceBundle = (
         limit: options.limit,
       }),
     );
+  if (options.detail === "links")
+    return ok(
+      inspectEvidenceLinks(bundle, options.filters, {
+        traversal: options.traversal,
+        linkStatus: options.link_status,
+        offset: options.offset,
+        limit: options.limit,
+      }),
+    );
   return ok(
     options.detail === "summary"
       ? summarizeEvidenceBundle(bundle, options.filters)

src/application/investigation/InvestigationEvidence.test.ts

@@ -5,7 +5,10 @@ import { createEvidenceBundle } from "../../domain/evidenceBundle.js";
 import { projectAnalysisError } from "../../domain/analysisErrorProjection.js";
 import { analysisErrorProjectionSchema } from "../../contracts/errorSchemas.js";
 import { InvestigationRecords } from "./InvestigationRecords.js";
-import { resolveInvestigationEvidenceClosure } from "./InvestigationEvidence.js";
+import {
+  createInvestigationEvidenceClosureChecker,
+  resolveInvestigationEvidenceClosure,
+} from "./InvestigationEvidence.js";
 
 const observation = (path: string, links: readonly string[] = []): Evidence =>
   createEvidence(
@@ -108,3 +111,50 @@ it("rejects a lookup that returns another semantic Evidence identity", () => {
     },
   });
 });
+
+it("resolves an authenticated source with a wide repeated-link array", () => {
+  const leaf = observation("/wide-leaf");
+  const source = observation(
+    "/wide-source",
+    Array(500_000).fill(leaf.evidence_id),
+  );
+  expect(source.evidence_links).toHaveLength(500_000);
+  const records = new InvestigationRecords();
+  for (const record of [leaf, source]) {
+    const added = records.recordEvidence(record);
+    if (!added.ok) throw added.error;
+  }
+  expect(
+    records.evidenceForAnalysis(source.evidence_id)?.evidence_links,
+  ).toHaveLength(500_000);
+  expect(
+    resolveInvestigationEvidenceClosure(records, [source.evidence_id]),
+  ).toEqual({
+    ok: true,
+    value: [source.evidence_id, leaf.evidence_id].sort(),
+  });
+});
+
+it("reuses a complete shared source graph without weakening missing-source checks", () => {
+  const leaf = observation("/shared-leaf");
+  const source = observation("/shared-source", [leaf.evidence_id]);
+  const records = new Map(
+    [leaf, source].map((record) => [record.evidence_id, record]),
+  );
+  let lookups = 0;
+  const check = createInvestigationEvidenceClosureChecker({
+    evidenceForAnalysis: (id) => {
+      lookups++;
+      return records.get(id);
+    },
+  });
+  expect(check([source.evidence_id])).toBe(true);
+  expect(lookups).toBe(2);
+  expect(check([source.evidence_id, leaf.evidence_id])).toBe(true);
+  expect(lookups).toBe(2);
+  const missing = `ev_${"0".repeat(64)}`;
+  expect(check([missing])).toBe(false);
+  expect(check([missing])).toBe(false);
+  expect(lookups).toBe(3);
+  expect(check([source.evidence_id, missing])).toBe(false);
+});

src/application/investigation/InvestigationEvidence.ts

@@ -5,6 +5,37 @@ import type { EvidenceIntegrityError } from "../../domain/evidenceErrors.js";
 import type { Evidence } from "../../domain/evidence.js";
 import { ok, type Result } from "../../domain/result.js";
 
+type Lookup = (id: string) => Evidence | undefined;
+
+/** Traverse without expanding a wide link array into function arguments. */
+const visitClosure = (
+  lookup: Lookup,
+  seedIds: readonly string[],
+  knownComplete?: ReadonlySet<string>,
+): Result<Set<string>, EvidenceIntegrityError> => {
+  const visited = new Set<string>();
+  const pending = [...seedIds];
+  while (pending.length > 0) {
+    const evidenceId = pending.pop();
+    if (
+      evidenceId === undefined ||
+      visited.has(evidenceId) ||
+      knownComplete?.has(evidenceId)
+    )
+      continue;
+    const evidence = resolveEvidenceInput(
+      { kind: "retained-evidence", evidence_id: evidenceId },
+      lookup,
+      "retained-closure",
+    );
+    if (!evidence.ok) return evidence;
+    visited.add(evidenceId);
+    for (const linkedId of evidence.value.evidence_links)
+      pending.push(linkedId);
+  }
+  return ok(visited);
+};
+
 /** Follow exact session references without exporting unrelated records or Unknowns. */
 export const resolveInvestigationEvidenceClosure = (
   reader: Pick<EvidenceReader, "evidenceForAnalysis">,
@@ -16,21 +47,32 @@ export const resolveInvestigationEvidenceClosure = (
   const supplied = new Map(
     sources.map((source) => [source.evidence_id, source]),
   );
-  const lookup = (id: string) =>
-    supplied.get(id) ?? reader.evidenceForAnalysis(id);
-  const visited = new Set<string>();
-  const pending = [...seedIds];
-  while (pending.length > 0) {
-    const evidenceId = pending.pop();
-    if (evidenceId === undefined || visited.has(evidenceId)) continue;
-    const evidence = resolveEvidenceInput(
-      { kind: "retained-evidence", evidence_id: evidenceId },
-      lookup,
-      "retained-closure",
+  const visited = visitClosure(
+    (id) => supplied.get(id) ?? reader.evidenceForAnalysis(id),
+    seedIds,
+  );
+  return visited.ok ? ok(uniqueSorted([...visited.value])) : visited;
+};
+
+/** Reuse closure decisions while the caller's lookup remains immutable. */
+export const createInvestigationEvidenceClosureChecker = (
+  reader: Pick<EvidenceReader, "evidenceForAnalysis">,
+): ((seedIds: readonly string[]) => boolean) => {
+  const complete = new Set<string>();
+  const incomplete = new Set<string>();
+  return (seedIds) => {
+    const single = seedIds.length === 1 ? seedIds[0] : undefined;
+    if (single !== undefined && incomplete.has(single)) return false;
+    const visited = visitClosure(
+      (id) => reader.evidenceForAnalysis(id),
+      seedIds,
+      complete,
     );
-    if (!evidence.ok) return evidence;
-    visited.add(evidenceId);
-    pending.push(...evidence.value.evidence_links);
-  }
-  return ok(uniqueSorted([...visited]));
+    if (!visited.ok) {
+      if (single !== undefined) incomplete.add(single);
+      return false;
+    }
+    for (const id of visited.value) complete.add(id);
+    return true;
+  };
 };

src/application/investigation/recordEvidenceSources.ts

@@ -5,7 +5,10 @@ import type { AnalysisError } from "../../domain/analysisErrorBase.js";
 import { AnalysisCapabilityUnavailableError } from "../../domain/analysisErrorCore.js";
 
 /** Source facts remain available even when a completed observation is cancelled. */
-export type AnalysisResultWithSources<Value> = Result<Value, AnalysisError> & {
+export type AnalysisResultWithSources<Value, Failure = AnalysisError> = Result<
+  Value,
+  Failure
+> & {
   readonly sourceEvidence?: readonly Evidence[];
 };
 

src/application/reverse/ReverseEngineeringService.ts

@@ -549,7 +549,7 @@ export class ReverseEngineeringService {
               ? "REA_OBJDUMP_COMMAND"
               : "REA_RIZIN_COMMAND";
           earlyFailure = new AnalysisCapabilityUnavailableError(
-            provider,
+            profile.identity.id,
             operation,
             `Unable to run configured command (${String(code ?? "unknown error")})`,
             {
@@ -708,10 +708,10 @@ export class ReverseEngineeringService {
     const limitations = [
       ...(absolutePath === undefined
         ? [
-            "The objdump version is not reported; the output lists BFD targets advertised by the installed tool and does not establish support for the selected artifact.",
+            "The objdump implementation and version are unknown. The captured output is the selected command's response and does not establish support for an artifact.",
           ]
         : [
-            "The executable version and supported formats are reported as unknown because no reliable version probe was performed.",
+            "The executable implementation, version and supported formats are unknown because no reliable identity probe was performed.",
           ]),
       "A non-zero process exit is preserved as an observed command result.",
       ...(operation === "inspect_with_objdump" &&
@@ -759,9 +759,7 @@ export class ReverseEngineeringService {
             `Command completion is unknown because the operation failed with ${failure._tag}: ${failure.message}`,
           ]),
       ...(absolutePath === undefined
-        ? [
-            "This output lists BFD targets advertised by the installed objdump and is independent of the selected artifact.",
-          ]
+        ? []
         : [
             "When both are available, pre-run and post-run digests detect artifact changes across the provider call but cannot prove the exact bytes consumed during the call.",
           ]),