fix(native): preserve signature uncertainty and validate ticket framing

2026-10-08 23:16:28 +08:00
commit c1535d88ab
@@ -28,7 +28,7 @@ intentionally not included. -->
 - Provider, bridge, target-format, or platform compatibility:
 - Evidence, artifact, provenance, or reconstruction contract:
 - Process execution, authorization, cleanup, or containment impact:
- Generated metadata (`docs/product-catalog.json`), package, or installation impact (the regen-generated bot pushes tracked generated files; never hand-edit them):
+- Generated metadata (`docs/public/product-catalog.json`), package, or installation impact (CI generates and validates ignored catalogs and `skills/`; edit authored instructions in `skill-src/` and never commit build outputs):

 ## Evidence and regression coverage

@@ -328,6 +328,8 @@ jobs:
        run: npm run test:focused -- tests/boundary/cli/nativeDemangleCli.test.ts tests/boundary/mcp/nativeDemangleMcp.test.ts
      - name: Process filesystem snapshot descriptor regressions
        run: npm run test:focused -- src/process/capture/FilesystemSnapshot.test.ts
+      - name: Native Darwin ownership and process cleanup regressions
+        run: npm run test:focused -- tests/boundary/process/darwinProcessRunTokenReader.test.ts tests/boundary/process/processCaptureLifecycle.test.ts tests/boundary/cli/processCli.test.ts tests/boundary/mcp/sessionMcp.test.ts

  reconstruction-readiness:
    name: Reconstruction readiness
@@ -442,6 +444,11 @@ jobs:
          tests/boundary/filesystem/safeOutputTree.test.ts
          tests/boundary/providers/native/artifactProvider.archiveSafety.test.ts
          tests/boundary/filesystem/setupUnavailableProvider.test.ts
+          tests/boundary/filesystem/windowsNpxRegistration.test.ts
+          src/application/ClientRegistrationIdentity.test.ts
+          tests/boundary/filesystem/webScriptManifestPaths.test.ts
+          tests/acceptance/webModuleCli.test.ts
+          tests/acceptance/webSourceLocationCli.test.ts
          tests/boundary/cli/referenceSourceImportStatus.test.ts
          src/cliReferenceSourceImportStatus.test.ts
          tests/boundary/filesystem/asarInventoryFreshness.test.ts
@@ -482,3 +489,13 @@ jobs:
          cache: npm
      - run: npm ci
      - run: npm run docs:check
+      - name: Generation leaves authored files unchanged
+        run: git diff --exit-code
+      - uses: actions/upload-artifact@v4
+        with:
+          name: generated-docs
+          path: |
+            docs/public/product-catalog.json
+            docs/verification/managed-conformance-*.json
+            skills/reverse-engineer-anything
+          if-no-files-found: error
@@ -1,75 +0,0 @@
-name: Regenerate generated metadata
-
-on:
-  pull_request:
-    branches: [main]
-    paths:
-      - "src/**"
-      - "skills/**/SKILL.md"
-      - "scripts/generate-*.mjs"
-      - "scripts/check-doc-facts.mjs"
-      - "scripts/lib/*.mjs"
-      - "scripts/verify/managed/**"
-      - "scripts/fixtures/managed/**"
-      - "package.json"
-      - "package-lock.json"
-
-concurrency:
-  group: regen-${{ github.event.pull_request.number }}
-  cancel-in-progress: true
-
-env:
-  HUSKY: "0"
-
-permissions:
-  contents: write
-
-jobs:
-  regen:
-    name: Regenerate and push tracked generated files
-    # Same-repo PRs only: the default token cannot push to forks.
-    # The bot-actor guard stops looped runs triggered by our own push.
-    if: >-
-      github.actor != 'github-actions[bot]' &&
-      github.event.pull_request.head.repo.full_name == github.repository
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          ref: ${{ github.event.pull_request.head.ref }}
-      - uses: actions/setup-node@v4
-        with:
-          node-version-file: .nvmrc
-          cache: npm
-      - run: npm ci
-      - run: npm run docs:generate
-      - name: Commit regenerated files
-        shell: bash
-        env:
-          HEAD_REF: ${{ github.event.pull_request.head.ref }}
-        run: |
-          generated_paths=(
-            docs/product-catalog.json
-            docs/error-contract.schema.json
-            docs/verification/managed-conformance-manifest.json
-            docs/verification/managed-conformance-ledger.json
-            skills/reverse-engineer-anything/SKILL.md
-            src/generatedPackageMetadata.ts
-          )
-          if git diff --quiet -- "${generated_paths[@]}"; then
-            echo "Generated metadata is already canonical."
-            exit 0
-          fi
-          git diff --check
-          # Refuse to sweep unrelated working-tree changes into the bot commit.
-          unexpected="$(git diff --name-only | grep -vxF -f <(printf '%s\n' "${generated_paths[@]}") || true)"
-          if [[ -n "${unexpected}" ]]; then
-            echo "docs:generate left unexpected tracked changes:" >&2
-            printf '%s\n' "${unexpected}" >&2
-            exit 1
-          fi
-          git config user.name "github-actions[bot]"
-          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
-          git add -- "${generated_paths[@]}"
-          git commit -m "chore: regenerate generated metadata"
-          git push origin "HEAD:${HEAD_REF}"
@@ -170,43 +170,9 @@ jobs:
        if: inputs.phase == 'prepare' && steps.release.outputs.prs_created == 'true'
        run: npm run docs:generate

-      - name: Commit canonical release catalog
+      - name: Validate generated release documentation
        if: inputs.phase == 'prepare' && steps.release.outputs.prs_created == 'true'
-        shell: bash
-        env:
-          # Use the same identity for the follow-up commit so it also triggers CI.
-          GH_TOKEN: ${{ secrets.RELEASE_PLEASE_TOKEN || secrets.GITHUB_TOKEN }}
-          RELEASE_PR_JSON: ${{ steps.release.outputs.pr }}
-        run: |
-          release_pr_branch="$(node --input-type=module -e '
-            const value = JSON.parse(process.env.RELEASE_PR_JSON ?? "");
-            if (
-              typeof value !== "object" ||
-              value === null ||
-              typeof value.headBranchName !== "string" ||
-              value.headBranchName.length === 0
-            ) {
-              process.exit(1);
-            }
-            process.stdout.write(value.headBranchName);
-          ')"
-          changed_paths="$(git diff --name-only)"
-          if [[ -z "${changed_paths}" ]]; then
-            echo "Release documentation is already canonical."
-            exit 0
-          fi
-          if [[ "${changed_paths}" != "docs/product-catalog.json" ]]; then
-            echo "docs:generate changed unexpected tracked paths:" >&2
-            printf '%s\n' "${changed_paths}" >&2
-            exit 1
-          fi
-          git diff --check
-          git config user.name "github-actions[bot]"
-          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
-          git add -- docs/product-catalog.json
-          git commit -m "chore: normalize release product catalog"
-          gh auth setup-git
-          git push origin "HEAD:${release_pr_branch}"
+        run: npm run docs:check && git diff --exit-code

  publish:
    name: Publish to npm
@@ -38,6 +38,7 @@ test-results.xml
 .turbo/
 .cache/
 docs/.vitepress/cache/
+docs/.vitepress/dist/

 # OS
 .DS_Store
@@ -51,3 +52,10 @@ Thumbs.db

 # Build-generated MCP tool catalog (regenerated by `npm run build`; never commit)
 src/generatedMcpToolCatalog.ts
+
+# Derived catalogs, portable conformance projections, and packaged skill bundles
+# (regenerated from this checkout by `npm run build:cached`; never commit)
+/skills/
+/docs/public/product-catalog.json
+/docs/verification/managed-conformance-manifest.json
+/docs/verification/managed-conformance-ledger.json
@@ -24,7 +24,7 @@ REA is a layered ESM TypeScript application. Dependencies flow inward from pure
 - `src/application/` composes shared CLI/MCP workflows; `src/server/` translates MCP requests; `src/cli.ts` and `src/main.ts` are the CLI and MCP entry points.
 - `src/process/` owns shared process lifecycle primitives, not provider wire protocols. `bridge/` contains provider-side adapters.
 - `tests/` contains unit, composition, boundary, acceptance, and conformance tests. `scripts/verify-*` and capability directories under `scripts/verify/` contain real-toolchain checks.
- `docs/product-catalog.json` is generated. Update its source contracts and regenerate it; do not edit it directly.
+- `docs/public/product-catalog.json`, `docs/verification/managed-conformance-*.json`, and `skills/` are ignored build outputs. Update source contracts and authored instructions in `skill-src/`, then run `npm run build:cached`; never commit derived catalog digests or portable conformance projections.
 - `src/generatedMcpToolCatalog.ts` is build-generated and gitignored. Never commit it; resolve any trace of it in merges by deleting it and running `npm run build:cached`.

 ## Build, Test, and Development Commands
@@ -36,7 +36,7 @@ REA is a layered ESM TypeScript application. Dependencies flow inward from pure
 - `npm run check:changed`: run cached static checks and source tests affected since the branch merge base (default `origin/main`).
 - `npm run check:fast`: run cached typecheck and lint checks.
 - `npm run check:pr`: opt into the complete local deterministic gate and generated-document checks for broad changes; CI owns full coverage. Routine iterations need focused tests and relevant checks, not the whole gate each time.
- `npm run docs:check`: check committed generated documents; `npm run docs:generate` regenerates them.
+- `npm run docs:check`: build and validate generated documents for the current checkout; `npm run docs:generate` regenerates them. CI retains ignored outputs as artifacts and does not push snapshot commits to feature branches.
 - For provider-dependent changes, see [docs/testing.md](docs/testing.md) and run the matching real-provider verification.
 - Keep each verification lane's prerequisites limited to the claim it checks. Use host-native fixtures for host/provider acceptance; put optional cross-target formats and their external toolchains in a separate lane. Preflight required commands and report the missing dependency and lane clearly.

@@ -35,7 +35,7 @@ links, and `npm run docs:preview` to preview that build at `/rea/`.
 Site navigation lives in `docs/.vitepress/config.ts`. Keep links to guides
 relative so they work on GitHub and the website; link to repository files
 outside `docs/` using their full GitHub URLs. Generated reference documents
-still use `npm run docs:generate`; `docs:build` only builds the website.
+use `npm run docs:generate`; `docs:build` generates them before building the website.

 Pull requests run `npm run docs:check`. `.github/workflows/pages.yml` is a
 manual VitePress build and does not publish. The public site at
@@ -74,8 +74,24 @@ require the matching real-provider `verify:*` lane.
 Formatting uses Oxfmt and the committed `.oxfmtrc.json`; generated sources use
 the same configuration. Pre-commit formats and lints staged files; pre-push runs
 `check:fast`.
-`docs:check` checks committed generated metadata. `docs:generate` regenerates
-those files, and the docs CI lane checks them.
+`docs:check` builds and validates generated metadata for the current checkout.
+The product catalog (`docs/public/product-catalog.json`), portable managed
+conformance projections (`docs/verification/managed-conformance-*.json`), and
+packaged skill (`skills/`) are ignored build outputs. Edit skill instructions
+and references in `skill-src/`; the build adds catalog-dependent metadata to
+the packaged copy without rewriting authored files. The generated manifest
+commits to that exact packaged skill bundle. It is a portable projection of
+the deterministic managed verifier, not a record of optional real-provider runs.
+CI validates these outputs and retains them as artifacts instead of pushing
+generated-only commits onto feature branches. Reviewed source metadata such as
+`src/generatedPackageMetadata.ts` and `docs/error-contract.schema.json` remains
+tracked and checked for freshness. Do not commit ignored generated outputs.
+The build-generated product catalog contains documented facts and their provider
+identity, rather than full runtime schema hashes. The managed skill contains
+instructions and inventory metadata; doctor compares its installed files with
+the canonical bundle. Schema-only fixes should not change these outputs or the
+skill commitment in the conformance manifest. Runtime schema identity remains
+available through doctor and `binary_session`.
 Real-provider execution remains uncached; deterministic builds use Turbo.

 Local `npm test` runs every deterministic Vitest project without coverage or
@@ -10,12 +10,16 @@

 [![npm version](https://img.shields.io/npm/v/rea-agents?style=flat-square&color=cb3837)](https://www.npmjs.com/package/rea-agents)
 [![CI](https://img.shields.io/github/actions/workflow/status/morluto/rea/ci.yml?branch=main&style=flat-square&label=CI)](https://github.com/morluto/rea/actions/workflows/ci.yml)
-[![MCP tool catalog](https://img.shields.io/badge/MCP-tool_catalog-5c4ee5?style=flat-square)](docs/product-catalog.json)
+[![MCP tool catalog](https://img.shields.io/badge/MCP-tool_catalog-5c4ee5?style=flat-square)](docs/mcp-contracts.md#generated-catalog)
 [![Node.js 22+](https://img.shields.io/badge/Node.js-22.19%2B-339933?style=flat-square&logo=nodedotjs&logoColor=white)](https://nodejs.org/)
 [![skills.sh](https://skills.sh/b/morluto/rea?style=flat-square)](https://skills.sh/morluto/rea/reverse-engineer-anything)
 [![MIT license](https://img.shields.io/badge/license-MIT-f4c430?style=flat-square)](LICENSE)
 [![Discord](https://img.shields.io/discord/1556595354999332884?logo=discord&logoColor=white&label=Discord&color=5865F2)](https://discord.gg/GkcryMnJDM)

+🎉 **20,000 GitHub stars — thank you!**
+
+Thanks to everyone using REA, reporting bugs, testing builds, and contributing fixes.
+
 <a href="https://trendshift.io/repositories/82054?utm_source=repository-badge&amp;utm_medium=badge&amp;utm_campaign=badge-repository-82054" target="_blank" rel="noopener noreferrer"><img src="https://trendshift.io/api/badge/repositories/82054" alt="morluto%2Frea | Trendshift" width="250" height="55"/></a>

 **[Website](https://morluto.github.io/rea/) · [Guides](https://morluto.github.io/rea/guides/) · [Showcases](https://morluto.github.io/rea/showcase/)**
@@ -296,7 +300,7 @@ For exact options, prerequisites and result contracts:
 - [Readiness and troubleshooting](docs/installation.md#check-readiness-for-your-task): diagnose one agent or analysis engine.
 - [CLI and Evidence](docs/cli.md): commands, provider selection, snapshots, import/export and exit statuses.
 - [MCP contracts](docs/mcp-contracts.md) and [agent prompts](docs/mcp-prompts.md): tool results, sessions and guided investigations.
- [Tool catalog](docs/product-catalog.json): generated inventory of tools, providers and CLI commands.
+- [Tool catalog](docs/mcp-contracts.md#generated-catalog): build-generated inventory of tools, providers and CLI commands.
 - [Roadmap](docs/roadmap.md): planned work and capability trackers.

 Report vulnerabilities through [SECURITY.md](SECURITY.md).
@@ -15,6 +15,10 @@
 [![MIT license](https://img.shields.io/badge/license-MIT-f4c430?style=flat-square)](LICENSE)
 [![Discord](https://img.shields.io/discord/1556595354999332884?logo=discord&logoColor=white&label=Discord&color=5865F2)](https://discord.gg/GkcryMnJDM)

+🎉 **وصلنا إلى 20,000 نجمة على GitHub، شكرًا لكم!**
+
+شكرًا لكل من يستخدم REA ويبلّغ عن الأخطاء ويختبر الإصدارات ويساهم في إصلاحها.
+
 <a href="https://trendshift.io/repositories/82054?utm_source=repository-badge&amp;utm_medium=badge&amp;utm_campaign=badge-repository-82054" target="_blank" rel="noopener noreferrer"><img src="https://trendshift.io/api/badge/repositories/82054" alt="morluto%2Frea | Trendshift" width="250" height="55"/></a>

 **[الموقع (بالإنجليزية)](https://morluto.github.io/rea/) · [أدلة الاستخدام](https://morluto.github.io/rea/guides/) · [دراسة حالة DX-Ball](https://morluto.github.io/rea/showcase/dx-ball/)**
@@ -15,6 +15,10 @@
 [![MIT license](https://img.shields.io/badge/license-MIT-f4c430?style=flat-square)](LICENSE)
 [![Discord](https://img.shields.io/discord/1556595354999332884?logo=discord&logoColor=white&label=Discord&color=5865F2)](https://discord.gg/GkcryMnJDM)

+🎉 **GitHub スターが 20,000 を突破しました。ありがとうございます！**
+
+REA を使い、問題を報告し、ビルドをテストし、修正を届けてくださる皆さんに感謝します。
+
 <a href="https://trendshift.io/repositories/82054?utm_source=repository-badge&amp;utm_medium=badge&amp;utm_campaign=badge-repository-82054" target="_blank" rel="noopener noreferrer"><img src="https://trendshift.io/api/badge/repositories/82054" alt="morluto%2Frea | Trendshift" width="250" height="55"/></a>

 **[ウェブサイト（英語）](https://morluto.github.io/rea/) · [ガイド](https://morluto.github.io/rea/guides/) · [DX-Ball の事例](https://morluto.github.io/rea/showcase/dx-ball/)**
@@ -15,6 +15,10 @@
 [![MIT license](https://img.shields.io/badge/license-MIT-f4c430?style=flat-square)](LICENSE)
 [![Discord](https://img.shields.io/discord/1556595354999332884?logo=discord&logoColor=white&label=Discord&color=5865F2)](https://discord.gg/GkcryMnJDM)

+🎉 **GitHub 스타 20,000개, 감사합니다!**
+
+REA를 사용하고, 버그를 제보하고, 빌드를 테스트하고, 수정에 기여해 주신 모든 분께 감사드립니다.
+
 <a href="https://trendshift.io/repositories/82054?utm_source=repository-badge&amp;utm_medium=badge&amp;utm_campaign=badge-repository-82054" target="_blank" rel="noopener noreferrer"><img src="https://trendshift.io/api/badge/repositories/82054" alt="morluto%2Frea | Trendshift" width="250" height="55"/></a>

 **[웹사이트(영문)](https://morluto.github.io/rea/) · [가이드](https://morluto.github.io/rea/guides/) · [DX-Ball 사례](https://morluto.github.io/rea/showcase/dx-ball/)**
@@ -15,6 +15,10 @@
 [![MIT license](https://img.shields.io/badge/license-MIT-f4c430?style=flat-square)](LICENSE)
 [![Discord](https://img.shields.io/discord/1556595354999332884?logo=discord&logoColor=white&label=Discord&color=5865F2)](https://discord.gg/GkcryMnJDM)

+🎉 **GitHub Star 突破 20,000，感谢大家！**
+
+感谢每一位使用 REA、反馈问题、测试构建和贡献修复的朋友。
+
 <a href="https://trendshift.io/repositories/82054?utm_source=repository-badge&amp;utm_medium=badge&amp;utm_campaign=badge-repository-82054" target="_blank" rel="noopener noreferrer"><img src="https://trendshift.io/api/badge/repositories/82054" alt="morluto%2Frea | Trendshift" width="250" height="55"/></a>

 **[网站（英文）](https://morluto.github.io/rea/) · [使用指南](https://morluto.github.io/rea/guides/) · [DX-Ball 案例](https://morluto.github.io/rea/showcase/dx-ball/)**
@@ -133,8 +133,6 @@ def project_record(state, secrets):
            for key, item in value.items():
                if not isinstance(key, str):
                    raise CaptureFailure("format", "Native record has a non-string dictionary key.", path)
-                if key == "__proto__":
-                    raise CaptureFailure("unsupported", "Native object contains a __proto__ member that the current JSON schema boundary cannot preserve.", path)
                if any(secret in key for secret in secrets):
                    # Validate the omitted subtree too, then discard all of its
                    # coordinates rather than inventing a replacement identity.
@@ -112,6 +112,31 @@ enum RunTokenReadError: Error {
  case ambiguousEnvironmentBoundary
 }

+@_silgen_name("csops")
+private func csops(
+  _ pid: Int32,
+  _ ops: UInt32,
+  _ addr: UnsafeMutableRawPointer?,
+  _ size: Int
+) -> Int32
+
+private let csOpsStatus: UInt32 = 0
+private let csPlatformBinary: UInt32 = 0x0400_0000
+
+/**
+ * Whether the target image is an Apple platform binary. Current macOS omits
+ * the environment of platform binaries from KERN_PROCARGS2 for every caller,
+ * so this distinguishes a policy-withheld environment from a process whose
+ * environment is genuinely absent or transiently unreadable.
+ */
+func isPlatformBinary(pid: Int32) -> Bool {
+  var flags: UInt32 = 0
+  let result = withUnsafeMutablePointer(to: &flags) { pointer in
+    csops(pid, csOpsStatus, UnsafeMutableRawPointer(pointer), MemoryLayout<UInt32>.size)
+  }
+  return result == 0 && (flags & csPlatformBinary) != 0
+}
+
 private func readRunToken(pid: Int32, pointerSize: Int) -> RunTokenObservation {
  var mib = [CTL_KERN, KERN_PROCARGS2, Int32(pid)]
  var size = 0
@@ -133,7 +158,12 @@ private func readRunToken(pid: Int32, pointerSize: Int) -> RunTokenObservation {
  } catch RunTokenReadError.invalidTokenEncoding {
    return unavailable(pid: pid, reason: "invalid_run_token_encoding")
  } catch RunTokenReadError.environmentUnavailable {
-    return unavailable(pid: pid, reason: "environment_unavailable")
+    return unavailable(
+      pid: pid,
+      reason: isPlatformBinary(pid: pid)
+        ? "platform_binary_environment_withheld"
+        : "environment_unavailable"
+    )
  } catch RunTokenReadError.appleVectorUnavailable {
    return unavailable(pid: pid, reason: "apple_vector_unavailable")
  } catch RunTokenReadError.ambiguousEnvironmentBoundary {
@@ -27,7 +27,7 @@ REA_PWNTOOLS_PYTHON=/absolute/isolated-env/bin/python \
 REA never installs Python, packages or GDB, changes a user init file, launches
 the selected object as a host process, or requests runtime library resolution. The Python process
 uses isolated mode and an owned cache. Exact upstream profiles are recorded in
-[upstream provenance](../third_party/pwntools/README.md).
+[upstream provenance](https://github.com/morluto/rea/blob/main/third_party/pwntools/README.md).

 ## Interpreting results

@@ -24,7 +24,7 @@ their distinct unavailable-provider or capability classification.
 The host must already provide util-linux `prlimit`, normally `/usr/bin/prlimit`;
 `REA_EVM_PRLIMIT_COMMAND` can select another absolute executable. REA installs
 no system tools and changes no user configuration. [Upstream provenance and
-license](../third_party/evmole/README.md) are packaged.
+license](https://github.com/morluto/rea/blob/main/third_party/evmole/README.md) are packaged.

 ## Evidence semantics

@@ -95,7 +95,7 @@ npx skills add morluto/rea --skill reverse-engineer-anything

 This installs agent instructions and bundled references, not REA MCP
 registration or analysis engines. Follow the skill's
-[conditional connection guide](https://github.com/morluto/rea/blob/main/skills/reverse-engineer-anything/SKILL.md#connect-only-when-needed).
+[conditional connection guide](https://github.com/morluto/rea/blob/main/skill-src/reverse-engineer-anything/SKILL.md#connect-only-when-needed).
 Working tools can be used immediately. If tools are missing, inspect the current
 client's registration with `doctor --client codex --json` (substitute its client
 ID), then plan repairs with `setup --client codex --dry-run --json`. Show and
@@ -25,7 +25,7 @@ part of the current tool set.

 This guide describes the implementation and verification of
 [ADR-0003](adr/0003-managed-code-evidence-and-provider-boundary.md). The canonical
-tool inventory is [`product-catalog.json`](https://github.com/morluto/rea/blob/main/docs/product-catalog.json).
+tool inventory is the [build-generated catalog](mcp-contracts.md#generated-catalog).

 ## Shipped scope

@@ -1,5 +1,15 @@
 # MCP runtime contracts

+## Generated catalog
+
+Run `npm run build:cached` in a source checkout to generate the machine-readable
+catalog at `docs/public/product-catalog.json`. The [catalog](product-catalog.json)
+is also included in documentation builds. PR CI retains it with the packaged
+skill and portable conformance projections in the `generated-docs` artifact.
+These outputs describe the exact source revision being built; they are not
+checked-in snapshots. For a running server, `binary_session` remains the
+authoritative source of catalog identity and tool availability.
+
 ## Identity and discovery

 `binary_session` reports the active package, server, SDK, and negotiated
@@ -102,6 +102,12 @@ run the same owned-process cleanup path. Settlement reports whether the
 sampled process group quiesced or whether cleanup was needed or unverifiable;
 sampling cannot prove that every short-lived or detached descendant was seen.

+When the host withholds an unrelated process’s ownership token, REA leaves that
+process untouched and records its PID and reason in `cleanup.unverified_processes`
+and process residual unknowns. Successful cleanup verifies the owned group;
+it does not attribute those unrelated processes. Related or otherwise unexplained
+unreadable processes still prevent successful cleanup.
+
 ## Compare two captures

 Compare saved capture Evidence with:
@@ -1,722 +0,0 @@
-{
-  "package": {
-    "name": "rea-agents",
-    "version": "6.0.0",
-    "sdk": {
-      "server": "2.3.1",
-      "client": "2.3.1",
-      "core": "2.3.1"
-    },
-    "skill_version": "33"
-  },
-  "tools": {
-    "total": 139,
-    "families": [
-      {
-        "id": "direct",
-        "surface": "official-proxy",
-        "count": 41,
-        "tools": [
-          "address_name",
-          "address_to_file_offset",
-          "annotate_native_function",
-          "comment",
-          "current_address",
-          "current_document",
-          "current_procedure",
-          "goto_address",
-          "inline_comment",
-          "inspect_native_data_type",
-          "inspect_native_instruction",
-          "inspect_native_load_image",
-          "list_bookmarks",
-          "list_documents",
-          "list_names",
-          "list_procedures",
-          "list_segments",
-          "list_strings",
-          "next_address",
-          "prev_address",
-          "procedure_address",
-          "procedure_assembly",
-          "procedure_callees",
-          "procedure_callers",
-          "procedure_info",
-          "procedure_pseudo_code",
-          "procedure_references",
-          "read_bytes",
-          "read_function_instructions",
-          "resolve_containing_procedure",
-          "resolve_native_call_targets",
-          "search_procedures",
-          "search_strings",
-          "set_address_name",
-          "set_addresses_names",
-          "set_bookmark",
-          "set_comment",
-          "set_current_document",
-          "set_inline_comment",
-          "unset_bookmark",
-          "xrefs"
-        ]
-      },
-      {
-        "id": "enhanced",
-        "surface": "enhanced",
-        "count": 14,
-        "tools": [
-          "analyze_function",
-          "analyze_swift_types",
-          "batch_decompile",
-          "binary_overview",
-          "find_xrefs_to_name",
-          "get_call_graph",
-          "get_objc_classes",
-          "get_objc_protocols",
-          "inspect_native_api",
-          "inspect_native_dispatch_metadata",
-          "trace_call_path",
-          "trace_feature",
-          "trace_native_ui_action",
-          "trace_native_values"
-        ]
-      },
-      {
-        "id": "native",
-        "surface": "native-provider",
-        "count": 10,
-        "tools": [
-          "capture_native_ui_scenario",
-          "demangle_swift",
-          "inspect_binary_layout",
-          "inspect_macho",
-          "inspect_plist",
-          "inspect_recorded_crash",
-          "inspect_signature",
-          "list_architectures",
-          "observe_native_calls",
-          "observe_native_ui"
-        ]
-      },
-      {
-        "id": "artifact",
-        "surface": "artifact-provider",
-        "count": 7,
-        "tools": [
-          "decode_interface_builder",
-          "extract_artifact",
-          "inspect_artifact",
-          "inspect_asset_catalog",
-          "inspect_evm_interface",
-          "inspect_keyed_archive",
-          "trace_dylib_resolution"
-        ]
-      },
-      {
-        "id": "managed",
-        "surface": "managed",
-        "count": 7,
-        "tools": [
-          "compare_managed_members",
-          "import_managed_reconstruction",
-          "inspect_managed_artifact",
-          "inspect_managed_members",
-          "inspect_managed_native_boundaries",
-          "project_managed_application_graph",
-          "verify_managed_native_boundaries"
-        ]
-      },
-      {
-        "id": "firmware",
-        "surface": "firmware-provider",
-        "count": 2,
-        "tools": ["extract_firmware", "inspect_firmware_regions"]
-      },
-      {
-        "id": "android",
-        "surface": "android-provider",
-        "count": 5,
-        "tools": [
-          "inspect_android_class",
-          "inspect_android_method",
-          "inspect_android_package",
-          "search_android_classes",
-          "trace_android_references"
-        ]
-      },
-      {
-        "id": "browser",
-        "surface": "browser-provider",
-        "count": 12,
-        "tools": [
-          "analyze_web_bundle",
-          "capture_browser_scenario",
-          "capture_web_screenshot",
-          "compare_web_captures",
-          "compare_web_screenshots",
-          "discover_webmcp_tools",
-          "inspect_web_event_listeners",
-          "inspect_web_network_capture",
-          "inspect_web_page",
-          "list_browser_targets",
-          "observe_web_execution",
-          "observe_web_session"
-        ]
-      },
-      {
-        "id": "electron",
-        "surface": "electron-provider",
-        "count": 5,
-        "tools": [
-          "analyze_javascript_application",
-          "capture_electron_scenario",
-          "inspect_electron_page",
-          "list_electron_targets",
-          "reconcile_javascript_runtime"
-        ]
-      },
-      {
-        "id": "javascript-runtime",
-        "surface": "runtime-provider",
-        "count": 2,
-        "tools": [
-          "list_javascript_runtime_targets",
-          "observe_javascript_runtime"
-        ]
-      },
-      {
-        "id": "application",
-        "surface": "application-workflow",
-        "count": 13,
-        "tools": [
-          "build_reconstruction_obligation_ledger",
-          "compare_application_versions",
-          "compare_javascript_export_shapes",
-          "compare_source_to_bundle",
-          "evaluate_reconstruction_coverage",
-          "export_web_scripts",
-          "project_android_application_graph",
-          "project_apple_application_graph",
-          "recover_javascript_sources",
-          "trace_application_feature",
-          "trace_javascript_semantics",
-          "trace_web_module_imports",
-          "trace_web_source_location"
-        ]
-      },
-      {
-        "id": "session",
-        "surface": "session",
-        "count": 21,
-        "tools": [
-          "binary_session",
-          "build_call_path",
-          "capture_process_scenario",
-          "close_binary",
-          "compare_artifacts",
-          "compare_bundles",
-          "compare_functions",
-          "compare_process_captures",
-          "correlate_static_and_runtime",
-          "export_evidence_bundle",
-          "find_changed_behavior",
-          "get_evidence_bundle",
-          "get_navigation_context",
-          "import_evidence_bundle",
-          "inspect_address_context",
-          "list_unknowns",
-          "open_binary",
-          "record_unknown",
-          "update_unknown",
-          "verify_reconstruction",
-          "verify_unknown_resolution"
-        ]
-      }
-    ]
-  },
-  "providers": [
-    {
-      "id": "binwalk",
-      "name": "Binwalk",
-      "version": "3.1.0",
-      "capabilities": ["inspect_firmware_regions"]
-    },
-    {
-      "id": "evmole-interface",
-      "name": "REA EVM interface adapter",
-      "version": "evmole@0.9.3",
-      "capabilities": ["inspect_evm_interface"]
-    },
-    {
-      "id": "ghidra",
-      "name": "Ghidra",
-      "version": null,
-      "capabilities": [
-        "address_name",
-        "address_to_file_offset",
-        "analyze_function",
-        "annotate_native_function",
-        "inspect_native_data_type",
-        "inspect_native_instruction",
-        "inspect_native_load_image",
-        "list_documents",
-        "list_names",
-        "list_procedures",
-        "list_segments",
-        "list_strings",
-        "procedure_address",
-        "procedure_assembly",
-        "procedure_callees",
-        "procedure_callers",
-        "procedure_info",
-        "procedure_pseudo_code",
-        "procedure_references",
-        "read_bytes",
-        "read_function_instructions",
-        "resolve_containing_procedure",
-        "resolve_native_call_targets",
-        "search_procedures",
-        "search_strings",
-        "xrefs"
-      ]
-    },
-    {
-      "id": "har-schema/lossless-json",
-      "name": "REA HAR capture adapter",
-      "version": "har-schema@2.0.0;jsonc-parser@3.3.1;lossless-json@4.3.1",
-      "capabilities": ["inspect_web_network_capture"]
-    },
-    {
-      "id": "hopper",
-      "name": "Hopper Disassembler",
-      "version": null,
-      "capabilities": [
-        "address_name",
-        "address_to_file_offset",
-        "analyze_function",
-        "comment",
-        "current_address",
-        "current_document",
-        "current_procedure",
-        "goto_address",
-        "inline_comment",
-        "list_bookmarks",
-        "list_documents",
-        "list_names",
-        "list_procedures",
-        "list_segments",
-        "list_strings",
-        "next_address",
-        "prev_address",
-        "procedure_address",
-        "procedure_assembly",
-        "procedure_callees",
-        "procedure_callers",
-        "procedure_info",
-        "procedure_pseudo_code",
-        "procedure_references",
-        "read_bytes",
-        "read_function_instructions",
-        "resolve_containing_procedure",
-        "search_procedures",
-        "search_strings",
-        "set_address_name",
-        "set_addresses_names",
-        "set_bookmark",
-        "set_comment",
-        "set_current_document",
-        "set_inline_comment",
-        "unset_bookmark",
-        "xrefs"
-      ]
-    },
-    {
-      "id": "ida",
-      "name": "IDA Pro MCP adapter",
-      "version": "1",
-      "capabilities": [
-        "analyze_function",
-        "list_procedures",
-        "list_strings",
-        "procedure_address",
-        "procedure_assembly",
-        "procedure_callees",
-        "procedure_callers",
-        "procedure_pseudo_code",
-        "read_function_instructions",
-        "search_procedures",
-        "search_strings",
-        "xrefs"
-      ]
-    },
-    {
-      "id": "jadx",
-      "name": "JADX headless",
-      "version": "0.7.1",
-      "capabilities": [
-        "inspect_android_class",
-        "inspect_android_method",
-        "inspect_android_package",
-        "search_android_classes",
-        "trace_android_references"
-      ]
-    },
-    {
-      "id": "mitmproxy-native-tnetstring",
-      "name": "REA offline native mitmproxy adapter",
-      "version": "12.2.3",
-      "capabilities": ["inspect_web_network_capture"]
-    },
-    {
-      "id": "native-macos",
-      "name": "macOS native inspection utilities",
-      "version": null,
-      "capabilities": [
-        "capture_native_ui_scenario",
-        "demangle_swift",
-        "inspect_macho",
-        "inspect_plist",
-        "inspect_signature",
-        "list_architectures",
-        "observe_native_calls",
-        "observe_native_ui"
-      ]
-    },
-    {
-      "id": "pwntools-elf",
-      "name": "REA pwntools ELF adapter",
-      "version": "pwntools@4.15.0;pyelftools@0.33;unicorn@2.1.2",
-      "capabilities": ["inspect_binary_layout", "inspect_recorded_crash"]
-    },
-    {
-      "id": "rea-android-application",
-      "name": "REA Android application workflows",
-      "version": "1",
-      "capabilities": ["project_android_application_graph"]
-    },
-    {
-      "id": "rea-apple-application",
-      "name": "REA Apple application workflows",
-      "version": "1",
-      "capabilities": ["project_apple_application_graph"]
-    },
-    {
-      "id": "rea-artifact-graph",
-      "name": "REA safe artifact graph provider",
-      "version": "1",
-      "capabilities": [
-        "decode_interface_builder",
-        "extract_artifact",
-        "inspect_artifact",
-        "inspect_asset_catalog",
-        "inspect_keyed_archive",
-        "trace_dylib_resolution"
-      ]
-    },
-    {
-      "id": "rea-cdp-browser",
-      "name": "REA Chrome DevTools Protocol observation provider",
-      "version": "2",
-      "capabilities": [
-        "analyze_web_bundle",
-        "capture_web_screenshot",
-        "compare_web_captures",
-        "compare_web_screenshots",
-        "discover_webmcp_tools",
-        "inspect_web_event_listeners",
-        "inspect_web_page",
-        "list_browser_targets",
-        "observe_web_execution",
-        "observe_web_session"
-      ]
-    },
-    {
-      "id": "rea-cdp-electron",
-      "name": "REA Electron file-page CDP observation provider",
-      "version": "1",
-      "capabilities": ["inspect_electron_page", "list_electron_targets"]
-    },
-    {
-      "id": "rea-dotnet-static",
-      "name": "REA managed static analysis provider",
-      "version": "1",
-      "capabilities": [
-        "inspect_managed_artifact",
-        "inspect_managed_members",
-        "inspect_managed_native_boundaries"
-      ]
-    },
-    {
-      "id": "rea-dotnet-workflows",
-      "name": "REA managed-code workflows",
-      "version": "1",
-      "capabilities": [
-        "compare_managed_members",
-        "import_managed_reconstruction",
-        "project_managed_application_graph",
-        "verify_managed_native_boundaries"
-      ]
-    },
-    {
-      "id": "rea-javascript-application",
-      "name": "REA JavaScript application analyzer",
-      "version": "1",
-      "capabilities": ["analyze_javascript_application"]
-    },
-    {
-      "id": "rea-javascript-application-workflows",
-      "name": "REA JavaScript application workflows",
-      "version": "1",
-      "capabilities": [
-        "build_reconstruction_obligation_ledger",
-        "compare_application_versions",
-        "compare_javascript_export_shapes",
-        "compare_source_to_bundle",
-        "evaluate_reconstruction_coverage",
-        "trace_application_feature",
-        "trace_javascript_semantics"
-      ]
-    },
-    {
-      "id": "rea-javascript-runtime-reconciliation",
-      "name": "REA JavaScript runtime reconciliation",
-      "version": "1",
-      "capabilities": ["reconcile_javascript_runtime"]
-    },
-    {
-      "id": "rea-playwright-browser-scenario",
-      "name": "REA Playwright browser scenario capture provider",
-      "version": "1",
-      "capabilities": ["capture_browser_scenario"]
-    },
-    {
-      "id": "rea-playwright-electron-active",
-      "name": "REA Playwright active Electron observation provider",
-      "version": "1",
-      "capabilities": ["capture_electron_scenario"]
-    },
-    {
-      "id": "rea-v8-inspector",
-      "name": "REA passive Node/Electron V8 Inspector provider",
-      "version": "1",
-      "capabilities": [
-        "list_javascript_runtime_targets",
-        "observe_javascript_runtime"
-      ]
-    },
-    {
-      "id": "rea-web-script-export",
-      "name": "REA captured script export",
-      "version": "1",
-      "capabilities": [
-        "export_web_scripts",
-        "trace_web_module_imports",
-        "trace_web_source_location"
-      ]
-    },
-    {
-      "id": "unblob",
-      "name": "Unblob",
-      "version": "26.6.4",
-      "capabilities": ["extract_firmware"]
-    },
-    {
-      "id": "wakaru",
-      "name": "Wakaru",
-      "version": "1.13.0",
-      "capabilities": ["recover_javascript_sources"]
-    }
-  ],
-  "setup_clients": [
-    {
-      "id": "claude_code",
-      "display_name": "Claude Code",
-      "format": "json",
-      "configuration": "managed"
-    },
-    {
-      "id": "claude_desktop",
-      "display_name": "Claude Desktop",
-      "format": "json",
-      "configuration": "managed"
-    },
-    {
-      "id": "codex",
-      "display_name": "Codex",
-      "format": "toml",
-      "configuration": "managed"
-    },
-    {
-      "id": "cursor",
-      "display_name": "Cursor",
-      "format": "json",
-      "configuration": "managed"
-    },
-    {
-      "id": "gemini_cli",
-      "display_name": "Gemini CLI",
-      "format": "json",
-      "configuration": "managed"
-    },
-    {
-      "id": "windsurf",
-      "display_name": "Windsurf",
-      "format": "json",
-      "configuration": "managed"
-    },
-    {
-      "id": "devin",
-      "display_name": "Devin",
-      "format": "json",
-      "configuration": "managed"
-    },
-    {
-      "id": "opencode",
-      "display_name": "OpenCode",
-      "format": "opencode",
-      "configuration": "managed"
-    },
-    {
-      "id": "antigravity",
-      "display_name": "Antigravity",
-      "format": "json",
-      "configuration": "managed"
-    },
-    {
-      "id": "copilot_cli",
-      "display_name": "GitHub Copilot CLI",
-      "format": "copilot_cli",
-      "configuration": "managed"
-    },
-    {
-      "id": "commandcode",
-      "display_name": "Command Code",
-      "format": "commandcode",
-      "configuration": "managed"
-    },
-    {
-      "id": "vscode",
-      "display_name": "VS Code",
-      "format": "vscode",
-      "configuration": "managed"
-    }
-  ],
-  "cli": {
-    "primary_count": 94,
-    "commands": [
-      "address-to-file-offset",
-      "analyze",
-      "analyze-javascript-application",
-      "analyze-web-bundle",
-      "annotate-native-function",
-      "build-reconstruction-obligation-ledger",
-      "capabilities",
-      "capture-browser-scenario",
-      "capture-electron-scenario",
-      "capture-native-ui-scenario",
-      "capture-process",
-      "capture-web-screenshot",
-      "compare",
-      "compare-application-versions",
-      "compare-javascript-export-shapes",
-      "compare-managed-members",
-      "compare-process-captures",
-      "compare-source-to-bundle",
-      "compare-web-captures",
-      "compare-web-screenshots",
-      "decode-interface-builder",
-      "decompile",
-      "demangle-swift",
-      "discover-webmcp-tools",
-      "doctor",
-      "evaluate-reconstruction-coverage",
-      "evidence-export",
-      "evidence-import",
-      "export-web-scripts",
-      "extract-artifact",
-      "extract-firmware",
-      "function",
-      "import-managed-reconstruction",
-      "import-reference-source",
-      "inspect",
-      "inspect-android-class",
-      "inspect-android-method",
-      "inspect-android-package",
-      "inspect-artifact",
-      "inspect-asset-catalog",
-      "inspect-binary-layout",
-      "inspect-electron-page",
-      "inspect-evm-interface",
-      "inspect-firmware-regions",
-      "inspect-keyed-archive",
-      "inspect-macho",
-      "inspect-managed-artifact",
-      "inspect-managed-members",
-      "inspect-managed-native-boundaries",
-      "inspect-native-api",
-      "inspect-native-data-type",
-      "inspect-native-dispatch-metadata",
-      "inspect-native-instruction",
-      "inspect-native-load-image",
-      "inspect-plist",
-      "inspect-recorded-crash",
-      "inspect-signature",
-      "inspect-web-event-listeners",
-      "inspect-web-network-capture",
-      "inspect-web-page",
-      "instructions",
-      "list-architectures",
-      "list-browser-targets",
-      "list-electron-targets",
-      "list-javascript-runtime-targets",
-      "observe-javascript-runtime",
-      "observe-native-calls",
-      "observe-native-ui",
-      "observe-web-execution",
-      "observe-web-session",
-      "project-android-application-graph",
-      "project-apple-application-graph",
-      "project-managed-application-graph",
-      "providers",
-      "read-bytes",
-      "reconcile-javascript-runtime",
-      "recover-javascript-sources",
-      "resolve-native-call-targets",
-      "search",
-      "search-android-classes",
-      "setup",
-      "trace",
-      "trace-android-references",
-      "trace-application-feature",
-      "trace-dylib-resolution",
-      "trace-javascript-semantics",
-      "trace-native-ui-action",
-      "trace-native-values",
-      "trace-web-module-imports",
-      "trace-web-source-location",
-      "uninstall",
-      "update",
-      "verify-managed-native-boundaries",
-      "xrefs"
-    ],
-    "aliases": [
-      {
-        "name": "compare-bundles",
-        "target": "compare"
-      }
-    ]
-  },
-  "runtime_catalog": {
-    "counts": {
-      "cli_commands": 94,
-      "mcp_tools": 139,
-      "mcp_prompts": 6
-    },
-    "digests": {
-      "tools_sha256": "f128dcd29092b44884ac315724394c9af393ec551964130b1317d3099b5cd9f7",
-      "prompts_sha256": "ef2de8814390b340623c32001610aa2709d90bed51537b6e562ab3abf144ab4d",
-      "combined_sha256": "5f32503e32d18b44866edeca37bec7c4b371b4c3f2c5c23f37ffefdb13f65f44",
-      "providers_sha256": "954b499c76514890062d2b6c936d73cb3a9c45412d522a081125a325e81cdec5"
-    }
-  }
-}
@@ -144,8 +144,8 @@ before cutting the next checkpoint; otherwise main retains the previous
 release baseline and can propose an already-published version again.

 After publication, open a PR from the release branch back to main. Preserve
-main's later implementation changes and resolve generated-file conflicts by
-regenerating from the combined contracts with the released package version.
+main's later implementation changes and regenerate ignored build outputs from
+the combined contracts with the released package version.
 Review and test this synchronization PR, then use a merge commit so the release
 tag remains in main's ancestry. Keep the released tag unchanged.

@@ -163,9 +163,12 @@ git merge-base --is-ancestor rea-agents-5.0.0 origin/main

 Close any superseded rolling release PR. Future releases repeat the checkpoint
 procedure from main; never resume automatic release-PR refreshes on main pushes.
-The generated-metadata workflow stays limited to pull requests into main so it
-does not push commits onto a frozen candidate. Preparation normalizes
-`docs/product-catalog.json` on the bot pull request.
+Preparation generates and validates the catalog, portable conformance
+projections, and packaged skill from the candidate checkout without committing
+them. The checkpoint validator binds tracked version authority to the source
+SHA; generated-catalog and package checks validate the derived representation.
+No generated-metadata workflow pushes follow-up commits onto feature or release
+branches.

 ## Partial publication and retries

@@ -1,105 +0,0 @@
-{
-  "ledger_id": "ecl_132e857a8a93f0b366cd72f9cfa1c338ffd4100460a7834ef69abff936c84472",
-  "records": [
-    {
-      "claim_id": "managed.application-graph-projection",
-      "status": "pass",
-      "evidence_ids": [
-        "ev_b061a5a559acb3748cb9784c637f6693f74faeb564ba2b11d6fc32619e757459"
-      ]
-    },
-    {
-      "claim_id": "managed.decompiler-reconstruction-import",
-      "status": "pass",
-      "evidence_ids": [
-        "ev_13f3401a3aaddc3f6d087ad160fa928374e142cdb9861254359b46865b8c992e"
-      ]
-    },
-    {
-      "claim_id": "managed.dotnet-framework-x86-pinvoke",
-      "status": "pass",
-      "evidence_ids": [
-        "ev_6f026216826ca06e080b77ff608f02634fa945fbd2e151b4cd261c1444f8bbb1"
-      ]
-    },
-    {
-      "claim_id": "managed.ilspy-reconstruction-oracle",
-      "status": "unsupported",
-      "evidence_ids": [
-        "ev_65a94c4de03f9c6ebdaff3f381cca377821f349d3ca6dfad47a31cc586fae939"
-      ]
-    },
-    {
-      "claim_id": "managed.malformed-metadata",
-      "status": "pass",
-      "evidence_ids": [
-        "ev_deae4259ea4395623176de40d06c2abcbc2b3a77f0bfb068d76e568d801f45a8"
-      ]
-    },
-    {
-      "claim_id": "managed.managed-native-verification",
-      "status": "pass",
-      "evidence_ids": [
-        "ev_0edcbbcaa1191a4e5324a437f739957b77f9ac45e7897724337f2d6d06b3f9d1"
-      ]
-    },
-    {
-      "claim_id": "managed.modern-dotnet-anycpu",
-      "status": "pass",
-      "evidence_ids": [
-        "ev_d1af50e8dc04cd589385769efd8758e82095425f6e9c1cc4bf2f530c6b434c93"
-      ]
-    },
-    {
-      "claim_id": "managed.mvid-and-token-drift",
-      "status": "pass",
-      "evidence_ids": [
-        "ev_5493f40bc875535488d789a490361abcc1f76bfbdf52536d09ff127442a8e854"
-      ]
-    },
-    {
-      "claim_id": "managed.not-managed",
-      "status": "pass",
-      "evidence_ids": [
-        "ev_03ce0cc0183ee0710f8120e837565129559ab3bc41927df326066370c2341699"
-      ]
-    },
-    {
-      "claim_id": "managed.operator-local-manifest",
-      "status": "unsupported",
-      "evidence_ids": [
-        "ev_9d3e50da1d372c55f46649e69eae702cbe8f0ba6a81d1e46afc3e1a284c81757"
-      ]
-    },
-    {
-      "claim_id": "managed.operator-manifest-self-test",
-      "status": "pass",
-      "evidence_ids": [
-        "ev_f974f4b9d039cda841894c6173cae86427ecef48f4e7a4d6c73edf7b23af2b2a"
-      ]
-    },
-    {
-      "claim_id": "managed.unicode-obfuscated-identifiers",
-      "status": "pass",
-      "evidence_ids": [
-        "ev_c4f38ce76d8359d92ee8e9442503e47b7913550442349a0df688bd274a3def67"
-      ]
-    },
-    {
-      "claim_id": "managed.x64-ready-to-run-native-body",
-      "status": "pass",
-      "evidence_ids": [
-        "ev_3e05ef1d6a796d3d4cb3372fe8e549efec759c59bf09d8ff660059a2e448cbc0"
-      ]
-    }
-  ],
-  "summary": {
-    "total": 13,
-    "pass": 11,
-    "fail": 0,
-    "unsupported": 2,
-    "truncated": 0,
-    "unknown": 0,
-    "complete": false
-  }
-}
@@ -1,201 +0,0 @@
-{
-  "manifest_id": "ecm_1e391ef1556bdd58a1b304ec175cda45670eeb66154394ccbfee5cd63852151a",
-  "verifier": {
-    "id": "rea-managed-conformance",
-    "version": "1"
-  },
-  "environment": {
-    "platform": "portable",
-    "architecture": "portable",
-    "runtime": "node",
-    "runtime_version": "portable"
-  },
-  "skill_digests": [
-    {
-      "skill_id": "reverse-engineer-anything",
-      "sha256": "c1895dc7a01dac0c470881c0b09194f8abc6e009bff6e658bb559d4f7bd0049d"
-    }
-  ],
-  "claims": [
-    {
-      "claim_id": "managed.application-graph-projection",
-      "scenario": {
-        "id": "managed-application-graph-projection",
-        "version": 1
-      },
-      "artifact_sha256s": [
-        "f17fe6286cb07c6385e786e0aa877564d44123197f02617dfec70c537a33e4ea"
-      ],
-      "provider": {
-        "id": "rea-managed-conformance",
-        "version": "1"
-      }
-    },
-    {
-      "claim_id": "managed.decompiler-reconstruction-import",
-      "scenario": {
-        "id": "decompiler-reconstruction-import",
-        "version": 1
-      },
-      "artifact_sha256s": [
-        "cead4cc99733e4e56a5fd0cec8a0813bbc24e249aa72a10eca4c47ee3b0e129d"
-      ],
-      "provider": {
-        "id": "rea-managed-conformance",
-        "version": "1"
-      }
-    },
-    {
-      "claim_id": "managed.dotnet-framework-x86-pinvoke",
-      "scenario": {
-        "id": "dotnet-framework-x86-pinvoke",
-        "version": 1
-      },
-      "artifact_sha256s": [
-        "f17fe6286cb07c6385e786e0aa877564d44123197f02617dfec70c537a33e4ea"
-      ],
-      "provider": {
-        "id": "rea-managed-conformance",
-        "version": "1"
-      }
-    },
-    {
-      "claim_id": "managed.ilspy-reconstruction-oracle",
-      "scenario": {
-        "id": "ilspy-reconstruction-oracle",
-        "version": 1
-      },
-      "artifact_sha256s": [],
-      "provider": {
-        "id": "rea-managed-conformance",
-        "version": "1"
-      }
-    },
-    {
-      "claim_id": "managed.malformed-metadata",
-      "scenario": {
-        "id": "malformed-metadata",
-        "version": 1
-      },
-      "artifact_sha256s": [
-        "827e10b6391d29edca48c191e2ddd79f3bc1165e46e4ba2f4edf41ab60f45e78"
-      ],
-      "provider": {
-        "id": "rea-managed-conformance",
-        "version": "1"
-      }
-    },
-    {
-      "claim_id": "managed.managed-native-verification",
-      "scenario": {
-        "id": "managed-native-verification",
-        "version": 1
-      },
-      "artifact_sha256s": [
-        "9999999999999999999999999999999999999999999999999999999999999999",
-        "f17fe6286cb07c6385e786e0aa877564d44123197f02617dfec70c537a33e4ea"
-      ],
-      "provider": {
-        "id": "rea-managed-conformance",
-        "version": "1"
-      }
-    },
-    {
-      "claim_id": "managed.modern-dotnet-anycpu",
-      "scenario": {
-        "id": "modern-dotnet-anycpu",
-        "version": 1
-      },
-      "artifact_sha256s": [
-        "92b588ae43d418117fa108c0004b5d0451f6112238d21bad8d75c0eb1da860f0"
-      ],
-      "provider": {
-        "id": "rea-managed-conformance",
-        "version": "1"
-      }
-    },
-    {
-      "claim_id": "managed.mvid-and-token-drift",
-      "scenario": {
-        "id": "mvid-and-token-drift",
-        "version": 1
-      },
-      "artifact_sha256s": [
-        "276395c671a656ab57d583158443c10de552dccfb37dc97cd013f673c0f86b43",
-        "ef009dab7424fdeba996f2524dbe86fd899c96394498cca0463fcfdb228c5572"
-      ],
-      "provider": {
-        "id": "rea-managed-conformance",
-        "version": "1"
-      }
-    },
-    {
-      "claim_id": "managed.not-managed",
-      "scenario": {
-        "id": "not-managed",
-        "version": 1
-      },
-      "artifact_sha256s": [
-        "de74dab8ab034054a811d4248efcda0bed505187a061a806e274ae87bc453754"
-      ],
-      "provider": {
-        "id": "rea-managed-conformance",
-        "version": "1"
-      }
-    },
-    {
-      "claim_id": "managed.operator-local-manifest",
-      "scenario": {
-        "id": "operator-local-manifest",
-        "version": 1
-      },
-      "artifact_sha256s": [],
-      "provider": {
-        "id": "rea-managed-conformance",
-        "version": "1"
-      }
-    },
-    {
-      "claim_id": "managed.operator-manifest-self-test",
-      "scenario": {
-        "id": "operator-manifest-self-test",
-        "version": 1
-      },
-      "artifact_sha256s": [
-        "cdc11ec7fd0f392e43b9b23971cb41ec49fd0a997fc33c24fcc553cd4386ae37"
-      ],
-      "provider": {
-        "id": "rea-managed-conformance",
-        "version": "1"
-      }
-    },
-    {
-      "claim_id": "managed.unicode-obfuscated-identifiers",
-      "scenario": {
-        "id": "unicode-obfuscated-identifiers",
-        "version": 1
-      },
-      "artifact_sha256s": [
-        "cead4cc99733e4e56a5fd0cec8a0813bbc24e249aa72a10eca4c47ee3b0e129d"
-      ],
-      "provider": {
-        "id": "rea-managed-conformance",
-        "version": "1"
-      }
-    },
-    {
-      "claim_id": "managed.x64-ready-to-run-native-body",
-      "scenario": {
-        "id": "x64-ready-to-run-native-body",
-        "version": 1
-      },
-      "artifact_sha256s": [
-        "e47402428322cdcb06f561036d7d108528cbc6e262d92a21f869218a20c80bfb"
-      ],
-      "provider": {
-        "id": "rea-managed-conformance",
-        "version": "1"
-      }
-    }
-  ]
-}
@@ -32,9 +32,9 @@ HAR uses unchanged `har-schema@2.0.0` draft-06 schemas, `ajv@8.20.0`,
 `lossless-json@4.3.1` numeric representations, pinned in the npm lockfile.
 Only the HAR 1.2 profile is supported. Unknown extensions remain reported
 evidence. Duplicate object keys, including equal values and escaped spellings,
-are rejected before materialization. A `__proto__` member returns an explicit
-unsupported-boundary error in both formats: the current shared JSON schema
-cannot preserve this member. Original capture files remain unchanged.
+are rejected before materialization. Prototype-named members such as
+`__proto__` are preserved as ordinary own JSON members without prototype
+mutation. Original capture files remain unchanged.
 The observed mitmproxy 12.2.3 `SaveHar` profile can emit `postData.text: null`
 for a missing request body. REA preserves that reported null, omitting the
 optional field only from its validation copy for this exact producer profile;
@@ -87,7 +87,7 @@
    "mcp-catalog:check": "node scripts/generate-mcp-tool-catalog.mjs --check",
    "prebuild": "npm run deps:check && npm run metadata:check",
    "build": "node scripts/run-exclusive.mjs build npm run build:unlocked",
-    "build:unlocked": "node scripts/clean-build-output.mjs && tsc -p tsconfig.build.json && node scripts/generate-mcp-tool-catalog.mjs",
+    "build:unlocked": "node scripts/clean-build-output.mjs && tsc -p tsconfig.build.json && node scripts/generate-mcp-tool-catalog.mjs && node scripts/generate-skill-metadata.mjs && node scripts/generate-product-catalog.mjs && node scripts/generate-completion-ledger.mjs",
    "precheck": "npm run deps:check",
    "check": "turbo run typecheck lint format:check knip metadata:check",
    "precheck:fast": "npm run deps:check",
@@ -180,7 +180,9 @@
    "config:print": "node scripts/print-mcp-config.mjs",
    "evidence:generate": "npm run build:cached && node scripts/generate-completion-ledger.mjs",
    "evidence:check": "npm run build:cached && node scripts/generate-completion-ledger.mjs --check",
+    "predocs:dev": "npm run docs:generate",
    "docs:dev": "vitepress dev docs",
+    "predocs:build": "npm run docs:generate",
    "docs:build": "vitepress build docs",
    "docs:preview": "vitepress preview docs",
    "docs:generate": "node scripts/run-exclusive.mjs docs npm run docs:generate:unlocked",
@@ -34,11 +34,6 @@
          "type": "json",
          "path": "server.json",
          "jsonpath": "$.packages[0].version"
-        },
-        {
-          "type": "json",
-          "path": "docs/product-catalog.json",
-          "jsonpath": "$.package.version"
        }
      ]
    }
@@ -30,7 +30,7 @@ const { stdout } = await exec(
  },
 );
 const verifierOutput = JSON.parse(stdout);
-// Managed conformance claims are host-independent. Keep the checked-in
+// Managed conformance claims are host-independent. Keep the generated
 // commitment reproducible across macOS, Linux, and Windows rather than
 // embedding the machine that happened to generate it.
 const portableCompletionReport = {
@@ -17,7 +17,7 @@ const lock = JSON.parse(
  await readFile(join(root, "package-lock.json"), "utf8"),
 );
 const skill = await readFile(
-  join(root, "skills/reverse-engineer-anything/SKILL.md"),
+  join(root, "skill-src/reverse-engineer-anything/SKILL.md"),
  "utf8",
 );
 const skillVersion = /^\s{2}version:\s*"([^"]+)"\s*$/mu.exec(skill)?.[1];
@@ -1,3 +1,4 @@
+import { mkdir } from "node:fs/promises";
 import { dirname, join } from "node:path";
 import { fileURLToPath } from "node:url";

@@ -14,8 +15,10 @@ for (const argument of arguments_)

 const root = join(dirname(fileURLToPath(import.meta.url)), "..");
 const catalog = await createProductCatalog(root);
+const path = join(root, "docs/public/product-catalog.json");
+if (!arguments_.has("--check")) await mkdir(dirname(path), { recursive: true });
 await ensureGeneratedFile({
-  path: join(root, "docs/product-catalog.json"),
+  path,
  source: await serializeProductCatalog(catalog),
  check: arguments_.has("--check"),
  generateCommand: "npm run docs:generate",
@@ -1,4 +1,4 @@
-import { readFile } from "node:fs/promises";
+import { mkdir, readFile, readdir, rm } from "node:fs/promises";
 import { dirname, join } from "node:path";
 import { fileURLToPath, pathToFileURL } from "node:url";

@@ -10,26 +10,69 @@ for (const argument of arguments_)
    throw new Error(`Unknown skill metadata option: ${argument}`);

 const root = join(dirname(fileURLToPath(import.meta.url)), "..");
-const path = join(root, "skills/reverse-engineer-anything/SKILL.md");
-const current = await readFile(path, "utf8");
+const sourceRoot = join(root, "skill-src/reverse-engineer-anything");
+const outputRoot = join(root, "skills/reverse-engineer-anything");
+const check = arguments_.has("--check");
+const current = (
+  await readFile(join(sourceRoot, "SKILL.md"), "utf8")
+).replaceAll("\r\n", "\n");
 const { CATALOG_IDENTITY } = await import(
  `${pathToFileURL(join(root, "dist/catalogIdentity.js")).href}?${String(Date.now())}`
 );
-const withCount = current.replace(
-  /^\s{2}tool_count:\s*\d+\s*$/mu,
-  `  tool_count: ${String(CATALOG_IDENTITY.counts.mcp_tools)}`,
+if (/^\s{2}(?:tool_count|catalog_digest):/mu.test(current))
+  throw new Error(
+    "Catalog metadata belongs in the generated skill, not skill-src",
+  );
+const versionLine = /^ {2}version: "[^"\r\n]+"$/mu;
+if (!versionLine.test(current))
+  throw new Error("Missing authored skill version");
+const source = current.replace(
+  versionLine,
+  `$&\n  tool_count: ${String(CATALOG_IDENTITY.counts.mcp_tools)}`,
 );
-const digestLine = `  catalog_digest: "${CATALOG_IDENTITY.digests.combined_sha256}"`;
-const source = /^\s{2}catalog_digest:/mu.test(withCount)
-  ? withCount.replace(
-      /^\s{2}catalog_digest:\s*"[a-f0-9]{64}"\s*$/mu,
-      digestLine,
-    )
-  : withCount.replace(/^(\s{2}tool_count:\s*\d+\s*)$/mu, `$1\n${digestLine}`);
+const paths = await filePaths(sourceRoot);
+// Rebuild this owned output directory so removed references cannot survive a build.
+if (!check) await rm(outputRoot, { recursive: true, force: true });
+for (const relativePath of paths) {
+  const path = join(outputRoot, relativePath);
+  if (!check) await mkdir(dirname(path), { recursive: true });
+  await ensureGeneratedFile({
+    path,
+    source:
+      relativePath === "SKILL.md"
+        ? source
+        : (await readFile(join(sourceRoot, relativePath), "utf8")).replaceAll(
+            "\r\n",
+            "\n",
+          ),
+    check,
+    generateCommand: "npm run docs:generate",
+  });
+}
+if (
+  check &&
+  JSON.stringify(await filePaths(outputRoot)) !== JSON.stringify(paths)
+)
+  throw new Error(
+    "Generated skill file inventory drifted; run npm run docs:generate",
+  );

-await ensureGeneratedFile({
-  path,
-  source,
-  check: arguments_.has("--check"),
-  generateCommand: "npm run docs:generate",
-});
+async function filePaths(directory, prefix = "") {
+  const paths = [];
+  for (const entry of (await readdir(directory, { withFileTypes: true })).sort(
+    (left, right) =>
+      left.name < right.name ? -1 : left.name > right.name ? 1 : 0,
+  )) {
+    const relativePath = prefix === "" ? entry.name : `${prefix}/${entry.name}`;
+    if (entry.isDirectory())
+      paths.push(
+        ...(await filePaths(join(directory, entry.name), relativePath)),
+      );
+    else if (entry.isFile()) paths.push(relativePath);
+    else
+      throw new Error(
+        `Skill bundle requires regular files or directories: ${relativePath}`,
+      );
+  }
+  return paths;
+}
@@ -77,7 +77,12 @@ export const documentationFactIssues = async (root, catalog) => {
    requireText(issues, path, content, "MCP-tool_catalog");
    if (path === "README.md") {
      requireText(issues, path, content, "(docs/installation.md");
-      requireText(issues, path, content, "(docs/product-catalog.json)");
+      requireText(
+        issues,
+        path,
+        content,
+        "(docs/mcp-contracts.md#generated-catalog)",
+      );
      continue;
    }
    for (const client of catalog.setup_clients)
@@ -99,11 +104,16 @@ export const documentationFactIssues = async (root, catalog) => {
    requireText(issues, installationPath, installation, client.display_name);

  const agents = await readFile(join(root, "AGENTS.md"), "utf8");
-  requireText(issues, "AGENTS.md", agents, "docs/product-catalog.json");
+  requireText(issues, "AGENTS.md", agents, "docs/public/product-catalog.json");

  const templatePath = ".github/pull_request_template.md";
  const template = await readFile(join(root, templatePath), "utf8");
-  requireText(issues, templatePath, template, "docs/product-catalog.json");
+  requireText(
+    issues,
+    templatePath,
+    template,
+    "docs/public/product-catalog.json",
+  );

  return issues;
 };
@@ -58,16 +58,16 @@ export const createProductCatalog = async (root) => {
    runtime_catalog: {
      counts: sources.catalogIdentity.CATALOG_IDENTITY.counts,
      digests: {
-        ...sources.catalogIdentity.CATALOG_IDENTITY.digests,
+        // Full runtime schema digests belong to server identity, not this facts projection.
        providers_sha256: providerCatalogDigest(providers),
      },
    },
  };
 };

-/** Stable checked-in representation of the product catalog. */
+/** Stable build-generated representation of the product catalog. */
 export const serializeProductCatalog = (catalog) =>
  formatGeneratedFile(
-    "docs/product-catalog.json",
+    "docs/public/product-catalog.json",
    JSON.stringify(catalog, null, 2),
  );
@@ -180,13 +180,8 @@ async function validateCandidate(git, sha, version, commits) {
    ["server.json", server.version],
    ["server.json rea-agents package", npmPackage.version],
  );
-  const catalog = await readJson(
-    git,
-    sha,
-    "docs/product-catalog.json",
-    z.object({ package: versionSchema }),
-  );
-  versions.push(["docs/product-catalog.json", catalog.package.version]);
+  // Catalogs are generated and checked from this candidate by the release job;
+  // they are not version authority stored in the immutable source tree.
  const generated = await git([
    "show",
    `${sha}:src/generatedPackageMetadata.ts`,
@@ -1169,7 +1169,7 @@ try {
      );
      const ownershipInspection =
        ["/usr/bin/ps", "/bin/ps"].includes(match[1]) &&
-        line.includes('["ps", "-axo", "pid=,ppid=,pgid=,stat=,command="]');
+        line.includes('["ps", "-axo", "pid=,ppid=,pgid=,uid=,stat=,command="]');
      assert.ok(
        [process.execPath, python].includes(match[1]) || ownershipInspection,
        `Unexpected attempted host execution: ${line}`,
@@ -474,7 +474,9 @@ try {
        );
        const ownershipInspection =
          ["/usr/bin/ps", "/bin/ps"].includes(match[1]) &&
-          line.includes('["ps", "-axo", "pid=,ppid=,pgid=,stat=,command="]');
+          line.includes(
+            '["ps", "-axo", "pid=,ppid=,pgid=,uid=,stat=,command="]',
+          );
        assert.ok(
          [
            process.execPath,
@@ -1,4 +1,5 @@
 import { join } from "node:path";
+import { CATALOG_IDENTITY } from "../dist/catalogIdentity.js";

 import { exec } from "./lib/verify-package-core.mjs";
 import { verifyPackedBridge } from "./verify-packed-bridge.mjs";
@@ -28,6 +29,26 @@ export async function verifyPackagePack({ root, workspace }) {
    throw new Error("package did not expose both rea command entry points");
  if (packedManifest.mcpName !== "io.github.morluto/rea")
    throw new Error("package did not retain its MCP Registry ownership marker");
+  if (packedFiles.some((path) => path.startsWith("package/skill-src/")))
+    throw new Error(
+      "package included authored skill sources instead of only the generated bundle",
+    );
+  const skill = (
+    await exec("tar", [
+      "-xOf",
+      join(root, tarball),
+      "package/skills/reverse-engineer-anything/SKILL.md",
+    ])
+  ).stdout;
+  if (
+    !skill.includes(
+      `  tool_count: ${String(CATALOG_IDENTITY.counts.mcp_tools)}\n`,
+    ) ||
+    skill.includes("  catalog_digest:")
+  )
+    throw new Error(
+      "packaged skill metadata did not match the catalog shipped in the package",
+    );
  if (
    packedFiles.some(
      (path) => path.includes("__pycache__") || path.endsWith(".pyc"),
@@ -260,14 +260,16 @@ try {
    );
    const original = await readFile(path);
    for (const mode of ["cli", "mcp"]) {
-      const error = await inspect(
-        mode,
-        { capture_path: path, format },
-        "unsupported_provider",
-      );
-      assert.ok(
-        JSON.stringify(error).includes("JSON schema boundary cannot preserve"),
-      );
+      const value = await inspect(mode, { capture_path: path, format });
+      const reported =
+        format === "har"
+          ? value.container.reported._extension
+          : value.records[0].reported.metadata;
+      assert.equal(Object.hasOwn(reported, "__proto__"), true);
+      assert.deepEqual(reported["__proto__"], { preserved: 7 });
+      assert.equal(Object.getPrototypeOf(reported), Object.prototype);
+      assert.equal(Reflect.get(Object.prototype, "preserved"), undefined);
+      if (format === "har") assert.equal(reported.constructor, "ordinary");
      assert.deepEqual(await readFile(path), original);
      cases++;
    }
@@ -79,7 +79,7 @@ export async function verifyCoreInspectionTrace({
          (line) =>
            /^execve\("\/(?:usr\/)?bin\/ps",/u.test(line) &&
            line.includes(
-              '["ps", "-axo", "pid=,ppid=,pgid=,stat=,command="]',
+              '["ps", "-axo", "pid=,ppid=,pgid=,uid=,stat=,command="]',
            ) &&
            line.endsWith(" = 0"),
        );
@@ -128,7 +128,9 @@ export async function verifyCoreInspectionTrace({
        const executable = await realpath(match[1]).catch(() => match[1]);
        const ownership =
          psPaths.has(match[1]) &&
-          line.includes('["ps", "-axo", "pid=,ppid=,pgid=,stat=,command="]');
+          line.includes(
+            '["ps", "-axo", "pid=,ppid=,pgid=,uid=,stat=,command="]',
+          );
        const iconv =
          iconvPaths.has(match[1]) && line.includes('["iconv", "-l"]');
        const version =
@@ -3,8 +3,6 @@ name: reverse-engineer-anything
 description: Reverse engineer native, managed, Electron/JavaScript, packaged, firmware, and browser targets with REA. Use shipped-artifact or requested runtime evidence to explain features, compare versions, decompile code, or guide a reconstruction. Skip REA for ordinary source-repository architecture analysis.
 metadata:
  version: "33"
-  tool_count: 139
-  catalog_digest: "5f32503e32d18b44866edeca37bec7c4b371b4c3f2c5c23f37ffefdb13f65f44"
 ---

 # REA
@@ -0,0 +1,52 @@
+import { expect, it } from "vitest";
+import { PRODUCT_IDENTITY } from "../identity.js";
+import {
+  isOwnedClientRegistrationCommand,
+  npxRegistrationCommand,
+} from "./ClientRegistrationIdentity.js";
+import { setupRegistrationCommand } from "./SetupHost.js";
+
+it("uses a Windows executable for npm-run setup and preserves POSIX launchers", () => {
+  expect(setupRegistrationCommand("win32", true)).toEqual([
+    "cmd.exe",
+    "/d",
+    "/c",
+    "npx",
+    "-y",
+    PRODUCT_IDENTITY.registrationPackageSpecifier,
+    "mcp",
+  ]);
+  for (const platform of ["linux", "darwin"] as const)
+    expect(setupRegistrationCommand(platform, true)).toEqual([
+      "npx",
+      "-y",
+      PRODUCT_IDENTITY.registrationPackageSpecifier,
+      "mcp",
+    ]);
+});
+
+it.each(
+  [
+    npxRegistrationCommand("win32"),
+    ["cmd", "/c", "npx", "-y", "rea-agents@5.0.0", "mcp"],
+    ["npx", "-y", "rea-agents@5.0.0", "mcp"],
+  ].map((command) => ({ command })),
+)("recognizes owned current and legacy launchers: $command", ({ command }) => {
+  expect(isOwnedClientRegistrationCommand(command)).toBe(true);
+});
+
+it.each(
+  [
+    ["cmd.exe", "/d", "/c", "node", "custom.js", "mcp"],
+    ["cmd.exe", "/k", "npx", "-y", "rea-agents@5.0.0", "mcp"],
+    ["cmd.exe", "/c", "npx -y rea-agents@5.0.0 mcp"],
+    ["cmd.exe", "/c", "npx", "-y", "another-package", "mcp"],
+    ["cmd.exe", "/c", "npx", "-y", "rea-agents@5.0.0", "mcp", "&", "other"],
+    ["cmd.exe", "/c", "npx", "-y", "rea-agents@5.0.0 & other", "mcp"],
+  ].map((command) => ({ command })),
+)(
+  "does not claim custom shell commands as REA-owned: $command",
+  ({ command }) => {
+    expect(isOwnedClientRegistrationCommand(command)).toBe(false);
+  },
+);
@@ -3,6 +3,28 @@ import { valid } from "semver";

 import { PRODUCT_IDENTITY } from "../identity.js";

+/** Resolve a pinned npx launcher that stdio clients can spawn on the host. */
+export const npxRegistrationCommand = (
+  platform: NodeJS.Platform = process.platform,
+): readonly string[] => {
+  const command = [
+    "npx",
+    "-y",
+    PRODUCT_IDENTITY.registrationPackageSpecifier,
+    "mcp",
+  ];
+  return platform === "win32" ? ["cmd.exe", "/d", "/c", ...command] : command;
+};
+
+const unwrapNpxCommand = (command: readonly string[]): readonly string[] => {
+  const executable = command[0]?.toLowerCase();
+  if (executable !== "cmd" && executable !== "cmd.exe") return command;
+  if (command[1]?.toLowerCase() === "/c") return command.slice(2);
+  if (command[1]?.toLowerCase() === "/d" && command[2]?.toLowerCase() === "/c")
+    return command.slice(3);
+  return [];
+};
+
 /** Check that one parsed command points to REA's MCP entry point. */
 export const isOwnedClientRegistrationCommand = (
  command: readonly string[],
@@ -27,15 +49,16 @@ export const isOwnedClientRegistrationCommand = (
      return true;
  }

+  const npxCommand = unwrapNpxCommand(command);
  if (
-    command.length !== 4 ||
-    command[0] !== "npx" ||
-    command[1] !== "-y" ||
-    command[3] !== "mcp"
+    npxCommand.length !== 4 ||
+    npxCommand[0] !== "npx" ||
+    npxCommand[1] !== "-y" ||
+    npxCommand[3] !== "mcp"
  )
    return false;

-  const packageReference = command[2] ?? "";
+  const packageReference = npxCommand[2] ?? "";
  if (
    packageReference === PRODUCT_IDENTITY.packageName ||
    packageReference === PRODUCT_IDENTITY.packageSpecifier ||
@@ -9,7 +9,10 @@ import { z } from "zod";

 import { PRODUCT_IDENTITY } from "../identity.js";
 import { MCP_STARTUP_POLICY } from "../mcpStartupPolicy.js";
-import { isOwnedClientRegistrationCommand } from "./ClientRegistrationIdentity.js";
+import {
+  isOwnedClientRegistrationCommand,
+  npxRegistrationCommand,
+} from "./ClientRegistrationIdentity.js";
 import { supportedClients } from "./SupportedClients.js";
 import type { SetupClient } from "./SupportedClients.js";

@@ -108,7 +111,12 @@ export const readClientRegistrationStatuses = async (
          client.name,
          client.configPath,
          command,
-          registrationAligned(registration, client, currentCommandPath)
+          registrationAligned(
+            registration,
+            client,
+            currentCommandPath,
+            options.platform ?? process.platform,
+          )
            ? "aligned"
            : "stale",
        ),
@@ -132,6 +140,7 @@ const registrationAligned = (
  registration: z.output<typeof registrationSchema>,
  client: SetupClient,
  currentCommandPath: string,
+  platform: NodeJS.Platform,
 ): boolean => {
  const command = [registration.command, ...registration.args];
  if (registration.disabled === true || registration.enabled === false)
@@ -160,12 +169,10 @@ const registrationAligned = (
    resolve(command[1] ?? "") === currentCommandPath
  )
    return true;
+  const npxCommand = npxRegistrationCommand(platform);
  if (
-    command.length === 4 &&
-    command[0] === "npx" &&
-    command[1] === "-y" &&
-    command[2] === PRODUCT_IDENTITY.registrationPackageSpecifier &&
-    command[3] === "mcp"
+    command.length === npxCommand.length &&
+    command.every((argument, index) => argument === npxCommand[index])
  )
    return true;
  return (
@@ -26,7 +26,8 @@ export const createDoctorHostFixture = (
    Promise.resolve({
      version: PRODUCT_IDENTITY.skillVersion,
      toolCount: CATALOG_IDENTITY.counts.mcp_tools,
-      catalogDigest: CATALOG_IDENTITY.digests.combined_sha256,
+      catalogDigest: null,
+      canonical: true,
    }),
  ...overrides,
 });
@@ -177,6 +177,7 @@ describe("doctor installation identity", () => {
            version: "10",
            toolCount: null,
            catalogDigest: null,
+            canonical: false,
          }),
      }),
    );
@@ -14,6 +14,7 @@ import {
  readLinuxDistribution,
  type LinuxDistribution,
 } from "./LinuxHopper.js";
+import { canonicalSkillNeedsInstall } from "./SetupSkill.js";
 import { CATALOG_IDENTITY } from "../catalogIdentity.js";
 import { PRODUCT_IDENTITY, SDK_IDENTITY } from "../identity.js";
 import {
@@ -95,11 +96,13 @@ export interface DoctorHost {
  ilspyCmdVersion?(path: string): Promise<string | undefined>;
 }

-/** Parsed identity committed by an installed REA skill. */
+/** Observed skill metadata and comparison with the packaged instruction bundle. */
 interface InstalledSkillIdentity {
  readonly version: string | null;
  readonly toolCount: number | null;
  readonly catalogDigest: string | null;
+  /** Whether all managed instruction and reference files match this package. */
+  readonly canonical: boolean;
 }

 /** Structured result returned by the read-only doctor workflow. */
@@ -139,6 +142,7 @@ interface DoctorIdentity {
  readonly skill: {
    readonly installed_version: string | null;
    readonly installed_tool_count: number | null;
+    /** Legacy catalog digest observed in older bundles; current bundles omit it. */
    readonly installed_catalog_digest: string | null;
    readonly state: "aligned" | "stale" | "missing";
    readonly remediation: string | null;
@@ -253,7 +257,7 @@ const skillIdentityAligned = (
 ): boolean =>
  identity?.version === PRODUCT_IDENTITY.skillVersion &&
  identity.toolCount === CATALOG_IDENTITY.counts.mcp_tools &&
-  identity.catalogDigest === CATALOG_IDENTITY.digests.combined_sha256;
+  identity.canonical;

 const skillIdentityCheck = (
  identity: InstalledSkillIdentity | undefined,
@@ -507,6 +511,7 @@ const installedSkillIdentity = async (
    const content = await readInstalledSkill(home);
    const countText = /^\s{2}tool_count:\s*(\d+)\s*$/mu.exec(content)?.[1];
    return {
+      canonical: !(await canonicalSkillNeedsInstall(home)),
      version: /^\s{2}version:\s*"([^"]+)"\s*$/mu.exec(content)?.[1] ?? null,
      toolCount:
        countText === undefined ? null : Number.parseInt(countText, 10),
@@ -1,4 +1,6 @@
 import {
+  describeEvidenceBundleFailure,
+  describeValidationFailure,
  parseEvidenceBundle,
  serializeEvidenceBundle,
  type EvidenceBundle,
@@ -20,20 +22,31 @@ export const readEvidenceBundle = async (
 ): Promise<Result<EvidenceBundle, EvidenceReadFailure>> => {
  const loaded = await readJsonFile(path);
  if (!loaded.ok) return loaded;
+  let bundle: EvidenceBundle;
  try {
-    const bundle = parseEvidenceBundle(loaded.value);
-    for (const record of bundle.records) {
-      if (record.predicate_type === "rea.process-capture")
-        parseProcessCapture(record.normalized_result);
-    }
-    return ok(bundle);
+    bundle = parseEvidenceBundle(loaded.value);
  } catch (cause: unknown) {
    return err(
      new EvidenceIntegrityError("Evidence bundle validation failed", {
        cause,
+        userMessage: describeEvidenceBundleFailure(loaded.value, cause),
      }),
    );
  }
+  for (const record of bundle.records) {
+    if (record.predicate_type !== "rea.process-capture") continue;
+    try {
+      parseProcessCapture(record.normalized_result);
+    } catch (cause: unknown) {
+      return err(
+        new EvidenceIntegrityError("Evidence bundle validation failed", {
+          cause,
+          userMessage: `Process capture record ${record.evidence_id} has an invalid normalized_result (${describeValidationFailure(cause)}). Recreate or re-export the bundle, then try again.`,
+        }),
+      );
+    }
+  }
+  return ok(bundle);
 };

 /** Atomically write deterministic evidence JSON at the caller-supplied path. */
@@ -10,10 +10,14 @@ import { err, ok, type Result } from "../domain/result.js";
 export const readJsonFile = async (
  path: string,
 ): Promise<Result<unknown, EvidenceFileError>> => {
+  const requestedPath = resolve(path);
  try {
-    const canonicalPath = await realpath(resolve(path));
+    const canonicalPath = await realpath(requestedPath);
    const stats = await lstat(canonicalPath);
-    if (!stats.isFile()) return err(new EvidenceFileError("read", "not-file"));
+    if (!stats.isFile())
+      return err(
+        new EvidenceFileError("read", "not-file", { path: requestedPath }),
+      );
    const encoded = await readFile(canonicalPath);
    let decoded: unknown;
    try {
@@ -23,11 +27,21 @@ export const readJsonFile = async (
        ),
      );
    } catch (cause: unknown) {
-      return err(new EvidenceFileError("read", "invalid-json", { cause }));
+      return err(
+        new EvidenceFileError("read", "invalid-json", {
+          cause,
+          path: requestedPath,
+        }),
+      );
    }
    return ok(decoded);
  } catch (cause: unknown) {
-    return err(new EvidenceFileError("read", "io", { cause }));
+    return err(
+      new EvidenceFileError("read", missingOrIo(cause), {
+        cause,
+        path: requestedPath,
+      }),
+    );
  }
 };

@@ -40,8 +54,8 @@ export const writeTextFile = async (
  Result<{ readonly path: string; readonly bytes: number }, EvidenceFileError>
 > => {
  const bytes = Buffer.byteLength(encoded, "utf8");
+  const requestedPath = resolve(path);
  try {
-    const requestedPath = resolve(path);
    const canonicalParent = await realpath(dirname(requestedPath));
    const destination = resolve(canonicalParent, basename(requestedPath));
    const existing = await lstat(destination).catch((cause: unknown) => {
@@ -49,9 +63,14 @@ export const writeTextFile = async (
      throw cause;
    });
    if (existing !== undefined) {
-      if (!overwrite) return err(new EvidenceFileError("write", "exists"));
+      if (!overwrite)
+        return err(
+          new EvidenceFileError("write", "exists", { path: requestedPath }),
+        );
      if (!existing.isFile() || existing.isSymbolicLink())
-        return err(new EvidenceFileError("write", "not-file"));
+        return err(
+          new EvidenceFileError("write", "not-file", { path: requestedPath }),
+        );
    }
    if (overwrite)
      await writeFileAtomic(destination, encoded, {
@@ -63,11 +82,27 @@ export const writeTextFile = async (
    return ok({ path: requestedPath, bytes });
  } catch (cause: unknown) {
    if (!overwrite && fileErrorCode(cause) === "EEXIST")
-      return err(new EvidenceFileError("write", "exists", { cause }));
-    return err(new EvidenceFileError("write", "io", { cause }));
+      return err(
+        new EvidenceFileError("write", "exists", {
+          cause,
+          path: requestedPath,
+        }),
+      );
+    return err(
+      new EvidenceFileError("write", missingOrIo(cause), {
+        cause,
+        path: requestedPath,
+      }),
+    );
  }
 };

+/** A missing path or parent is a selection error, not a permission failure. */
+const missingOrIo = (cause: unknown): "missing" | "io" => {
+  const code = fileErrorCode(cause);
+  return code === "ENOENT" || code === "ENOTDIR" ? "missing" : "io";
+};
+
 const publishNewFile = async (
  destination: string,
  encoded: string,
@@ -15,6 +15,7 @@ import { dirname } from "node:path";
 import writeFileAtomic from "write-file-atomic";

 import { PRODUCT_IDENTITY } from "../identity.js";
+import { npxRegistrationCommand } from "./ClientRegistrationIdentity.js";
 import { MCP_STARTUP_POLICY } from "../mcpStartupPolicy.js";
 import { resolveClientConfigTransactionPath } from "./ClientConfigPath.js";
 import type {
@@ -24,12 +25,7 @@ import type {
 } from "./SetupTypes.js";
 import type { SetupClient } from "./SupportedClients.js";

-const defaultCommand = (): readonly string[] => [
-  "npx",
-  "-y",
-  PRODUCT_IDENTITY.registrationPackageSpecifier,
-  "mcp",
-];
+const defaultCommand = (): readonly string[] => npxRegistrationCommand();

 /** Back up, atomically update, and semantically read back one JSON MCP configuration. */
 export const configureJsonClient = (
@@ -3,6 +3,7 @@ import { homedir } from "node:os";
 import { resolve } from "node:path";

 import { PRODUCT_IDENTITY } from "../identity.js";
+import { npxRegistrationCommand } from "./ClientRegistrationIdentity.js";
 import {
  SUPPORTED_NODE_VERSION_PROSE,
  supportsNodeVersion,
@@ -35,7 +36,7 @@ export const setupRegistrationCommand = (
  useNpmRunner: boolean = process.env.npm_command === "exec",
 ): readonly string[] =>
  useNpmRunner
-    ? PRODUCT_IDENTITY.mcpCommand.split(" ")
+    ? npxRegistrationCommand(platform)
    : platform === "win32"
      ? [
          process.execPath,
@@ -2,6 +2,7 @@ import canonicalize from "canonicalize";

 import {
  createEvidenceBundle,
+  describeEvidenceBundleFailure,
  parseEvidenceBundle,
  validateResidualUnknownAddition,
  type EvidenceBundle,
@@ -68,6 +69,7 @@ export class EvidenceLedger {
      return err(
        new EvidenceIntegrityError("Evidence bundle validation failed", {
          cause,
+          userMessage: describeEvidenceBundleFailure(input, cause),
        }),
      );
    }
@@ -21,7 +21,10 @@ import {
  type ArtifactAnalysisOperation,
 } from "../contracts/artifactToolContracts.js";
 import type { BinaryTarget } from "../domain/binaryTarget.js";
-import { AnalysisCapabilityUnavailableError } from "../domain/analysisErrorCore.js";
+import {
+  AnalysisCapabilityUnavailableError,
+  AnalysisInputError,
+} from "../domain/analysisErrorCore.js";
 import { ArtifactOperationError } from "../domain/artifactOperationError.js";
 import { type AnalysisError } from "../domain/analysisErrorBase.js";
 import type { JsonValue } from "../domain/jsonValue.js";
@@ -116,10 +119,15 @@ class ArtifactClient implements AnalysisClient {
          parameters.path !== "." &&
          parameters.path !== basename(this.target.path)
        )
-          throw new ArtifactReaderFailure(
-            "path",
-            "For an active plist, path must select that archive (omit path or use its basename)",
-          );
+          throw new AnalysisInputError(operation, undefined, [
+            {
+              path: ["path"],
+              reason: "invalid_value",
+              message:
+                "For an active plist, path must select that archive (omit path or use its basename).",
+              expected: basename(this.target.path),
+            },
+          ]);
        const bundlePath = standalone
          ? dirname(this.target.path)
          : this.target.sourcePath;
@@ -352,6 +360,8 @@ const translateFailure = (
      cause.details,
      cause.message,
    );
+  // Caller-selection failures are already typed; keep their correction details.
+  if (cause instanceof AnalysisInputError) return cause;
  return new ArtifactOperationError(operation, "io");
 };

@@ -1,6 +1,14 @@
+import { mkdir, symlink, writeFile } from "node:fs/promises";
+import { join } from "node:path";
+
 import { describe, expect, it } from "vitest";

-import { collectInterfaceBuilderResourceKeys } from "./AppleAssetCatalogAnalysis.js";
+import { createTestTempDirectory } from "../../../tests/fixtures/temporaryDirectory.js";
+import { ArtifactReaderFailure } from "../ArtifactReader.js";
+import {
+  analyzeAppleAssetCatalogs,
+  collectInterfaceBuilderResourceKeys,
+} from "./AppleAssetCatalogAnalysis.js";

 describe("Apple asset catalog application workflow", () => {
  it("joins only explicit resource-key fields with archive provenance", () => {
@@ -40,4 +48,70 @@ describe("Apple asset catalog application workflow", () => {
      },
    ]);
  });
+
+  it("reports an app without compiled catalogs as an empty observed inventory", async () => {
+    const bundle = await createTestTempDirectory("rea-asset-catalog-absent-");
+    await mkdir(join(bundle, "Contents", "Resources"), { recursive: true });
+    await writeFile(join(bundle, "Contents", "Resources", "icon.icns"), "");
+    const result = await analyzeAppleAssetCatalogs({
+      bundlePath: bundle,
+      targetSha256: "a".repeat(64),
+      runAssetUtil: () => {
+        throw new Error("assetutil must not run without a catalog");
+      },
+    });
+    expect(result).toMatchObject({
+      catalogs: [],
+      total_records: 0,
+      records: [],
+      resource_key_matches: [],
+      next_offset: null,
+      truncated: false,
+    });
+    expect(result.limitations).toContain(
+      "No compiled Assets.car catalog was found among the app bundle's regular files (symlinks are not followed); any resource keys are reported as unmatched.",
+    );
+  });
+
+  it("does not report absence when the only catalog entry is a symlink", async () => {
+    const bundle = await createTestTempDirectory("rea-asset-catalog-link-");
+    const resources = join(bundle, "Contents", "Resources");
+    await mkdir(resources, { recursive: true });
+    await writeFile(join(bundle, "outside.car"), "catalog");
+    await symlink("../../outside.car", join(resources, "Assets.car"));
+    const rejected = await analyzeAppleAssetCatalogs({
+      bundlePath: bundle,
+      targetSha256: "a".repeat(64),
+      runAssetUtil: () => Promise.resolve("[]"),
+    }).catch((cause: unknown) => cause);
+    expect(rejected).toBeInstanceOf(ArtifactReaderFailure);
+    expect(rejected).toMatchObject({
+      reason: "path",
+      message: expect.stringContaining(
+        "Contents/Resources/Assets.car (symlink)",
+      ),
+    });
+  });
+
+  it("discloses skipped catalog entries beside inspected catalogs", async () => {
+    const bundle = await createTestTempDirectory("rea-asset-catalog-mixed-");
+    const resources = join(bundle, "Contents", "Resources");
+    await mkdir(join(resources, "Nested"), { recursive: true });
+    await writeFile(join(resources, "Assets.car"), "catalog");
+    await symlink("../Assets.car", join(resources, "Nested", "Assets.car"));
+    const result = await analyzeAppleAssetCatalogs({
+      bundlePath: bundle,
+      targetSha256: "a".repeat(64),
+      runAssetUtil: () => Promise.resolve("[]"),
+    });
+    expect(result.catalogs.map(({ path }) => path)).toEqual([
+      "Contents/Resources/Assets.car",
+    ]);
+    expect(result.limitations).toContainEqual(
+      expect.stringContaining("Contents/Resources/Nested/Assets.car (symlink)"),
+    );
+    expect(result.limitations).not.toContainEqual(
+      expect.stringContaining("No compiled Assets.car catalog"),
+    );
+  });
 });
@@ -48,10 +48,15 @@ export const analyzeAppleAssetCatalogs = async (input: {
    sha256: string;
    records: ReturnType<typeof parseAppleAssetCatalogRecords>;
  }[] = [];
+  const uninspected: string[] = [];
  let totalMetadataBytes = 0;
  try {
    for await (const entry of reader.entries(input.signal)) {
-      if (entry.kind !== "file" || !entry.path.endsWith("Assets.car")) continue;
+      if (!entry.path.endsWith("Assets.car")) continue;
+      if (entry.kind !== "file") {
+        uninspected.push(`${entry.path} (${entry.kind})`);
+        continue;
+      }
      const inspected = await inspectAssetCatalogEntry({
        reader,
        entry,
@@ -69,10 +74,12 @@ export const analyzeAppleAssetCatalogs = async (input: {
  } finally {
    await reader.close();
  }
-  if (catalogs.length === 0)
+  // Without any readable catalog, unmatched resource keys would overstate an
+  // absence that a skipped catalog entry may contradict.
+  if (catalogs.length === 0 && uninspected.length > 0)
    throw new ArtifactReaderFailure(
-      "unavailable",
-      "No compiled Assets.car catalogs were found in the app bundle",
+      "path",
+      `Asset catalog entries are not regular files and were not inspected: ${uninspected.join(", ")}`,
    );
  const interfaceBuilder = await analyzeInterfaceBuilderBundle({
    bundlePath: input.bundlePath,
@@ -93,6 +100,18 @@ export const analyzeAppleAssetCatalogs = async (input: {
    ...result,
    limitations: [
      ...result.limitations,
+      // An app without a compiled catalog is an observed empty inventory, not
+      // a missing host tool.
+      ...(catalogs.length === 0
+        ? [
+            "No compiled Assets.car catalog was found among the app bundle's regular files (symlinks are not followed); any resource keys are reported as unmatched.",
+          ]
+        : []),
+      ...(uninspected.length === 0
+        ? []
+        : [
+            `Asset catalog entries that are not regular files were not inspected, so resource keys reported as unmatched may resolve there: ${uninspected.join(", ")}`,
+          ]),
      "Exact resource-key joins use only recognized image or asset key fields on decoded Interface Builder resource objects; other archive resource references are not inferred.",
      ...(interfaceBuilder.graph.truncated
        ? [
@@ -125,6 +125,16 @@ describe("inert keyed archive decoding", () => {
        offset: 0,
        limit: 1,
      }),
-    ).toThrow("does not exist");
+    ).toThrow(
+      expect.objectContaining({
+        issues: [
+          expect.objectContaining({
+            path: ["root"],
+            message: expect.stringContaining("does not exist"),
+            expected: ["root", "other"],
+          }),
+        ],
+      }),
+    );
  });
 });
@@ -2,6 +2,7 @@ import { createHash } from "node:crypto";
 import { TextDecoder } from "node:util";
 import { parseBinary } from "plist";
 import { z } from "zod";
+import { AnalysisInputError } from "../../domain/analysisErrorCore.js";
 import type { JsonValue } from "../../domain/jsonValue.js";
 import { projectPlistValue } from "../../domain/apple/plistValue.js";
 import {
@@ -25,6 +26,10 @@ export const decodeKeyedArchiveBytes = (
 ) => {
  if (bytes.length > MAX_BYTES)
    throw new RangeError("Keyed archive exceeds 64 MiB");
+  if (bytes.subarray(0, 10).toString("ascii") === "NIBArchive")
+    throw new TypeError(
+      "Selected file is a compiled NIBArchive, not a Foundation plist archive; decode it with decode_interface_builder",
+    );
  const binary = bytes.subarray(0, 8).toString("ascii") === "bplist00";
  const parsed = binary
    ? { value: parseBinary(bytes), omittedPrototypeKeys: 0 }
@@ -83,18 +88,20 @@ export const inspectBundleKeyedArchive = async (input: {
      .split("/")
      .some((part) => part === ".." || part === "." || part.length === 0)
  )
-    throw new ArtifactReaderFailure(
-      "path",
-      "Archive path must be a canonical relative bundle path",
+    throw archivePathError(
+      "invalid_format",
+      selected.path === "."
+        ? "Select a keyed archive path relative to the active app bundle."
+        : `Archive path must be a canonical relative bundle path without empty, '.', or '..' segments: ${selected.path}`,
    );
  const reader = new DirectoryArtifactReader(input.bundlePath);
  try {
    for await (const entry of reader.entries(input.signal)) {
      if (entry.path !== selected.path) continue;
      if (entry.kind !== "file")
-        throw new ArtifactReaderFailure(
-          "path",
-          "Archive must be a regular file, not a symlink or directory",
+        throw archivePathError(
+          "invalid_value",
+          `Archive path selects a ${entry.kind}, not a regular file: ${selected.path}`,
        );
      if ((entry.declaredSize ?? 0) > MAX_BYTES)
        throw new ArtifactReaderFailure(
@@ -132,18 +139,28 @@ export const inspectBundleKeyedArchive = async (input: {
          ...decodeKeyedArchiveBytes(bytes, selected),
        });
      } catch (cause) {
+        if (cause instanceof AnalysisInputError) throw cause;
        throw new ArtifactReaderFailure(
          cause instanceof RangeError ? "limit" : "format",
-          "Cannot decode selected Foundation keyed archive",
+          `Cannot decode selected Foundation keyed archive: ${cause instanceof Error ? cause.message : String(cause)}`,
          { cause },
        );
      }
    }
-    throw new ArtifactReaderFailure(
-      "path",
-      `Archive not found in bundle: ${selected.path}`,
+    throw archivePathError(
+      "invalid_value",
+      `No regular file exists at ${selected.path} in the active app bundle.`,
    );
  } finally {
    await reader.close();
  }
 };
+
+/** A caller-selected archive path, not the artifact, failed its constraint. */
+const archivePathError = (
+  reason: "invalid_format" | "invalid_value",
+  message: string,
+) =>
+  new AnalysisInputError("inspect_keyed_archive", undefined, [
+    { path: ["path"], reason, message },
+  ]);
@@ -26,6 +26,7 @@ import {
  type OwnedProcessGroup,
  type ProcessCleanupResult,
  type ProcessLineageObservation,
+  type OwnershipSweepUnverifiedProcess,
 } from "../process/ProcessOwnership.js";
 import {
  observeOwnedProcessLineage,
@@ -238,6 +239,17 @@ export class PlaywrightElectronActiveProvider implements ElectronActiveObservati
          ),
        );
      if (closeError !== undefined) return err(providerError(closeError));
+      if (outcome.ok && cleanup.unverified !== undefined)
+        outcome = ok({
+          ...outcome.value,
+          limitations: [
+            ...outcome.value.limitations,
+            ...cleanup.unverified.map(
+              ({ pid, diagnostic }) =>
+                `Ownership of unrelated process ${String(pid)} could not be verified; it was left untouched: ${diagnostic}`,
+            ),
+          ],
+        });
    }
    return outcome;
  }
@@ -280,6 +292,7 @@ const cleanupElectronProcesses = async (
    })),
  );
  let signaled = false;
+  const unverified: OwnershipSweepUnverifiedProcess[] = [];
  for (const processGroupId of groupIds) {
    const cleanupOwnership: OwnedProcessGroup =
      processGroupId === ownership.processGroupId
@@ -292,14 +305,38 @@ const cleanupElectronProcesses = async (
    const result = await cleanupOwnedProcessGroup(cleanupOwnership);
    if (!result.cleaned) return result;
    signaled ||= result.signaled;
+    unverified.push(...(result.unverified ?? []));
  }
  const remaining = await verifyNoTokenOwnedProcesses(
    ownership.runId,
    undefined,
    ownership.captureBaseline,
+    {
+      leaderPid: ownership.leaderPid,
+      processGroupId: ownership.processGroupId,
+      ...(ownership.sampledProcessGroupIds === undefined
+        ? {}
+        : { sampledProcessGroupIds: ownership.sampledProcessGroupIds }),
+    },
  );
  if (!remaining.cleaned) return remaining;
-  return { cleaned: true, signaled };
+  unverified.push(...(remaining.unverified ?? []));
+  return {
+    cleaned: true,
+    signaled,
+    ...(unverified.length === 0
+      ? {}
+      : {
+          unverified: [
+            ...new Map(
+              unverified.map((item) => [
+                `${String(item.pid)}:${item.diagnostic}`,
+                item,
+              ]),
+            ).values(),
+          ],
+        }),
+  };
 };

 const createResult = (
@@ -1,5 +1,5 @@
 import { lstat, realpath } from "node:fs/promises";
-import { dirname, isAbsolute, join, relative, sep } from "node:path";
+import { dirname, isAbsolute, join, relative, resolve, sep } from "node:path";
 import { ArtifactReaderFailure } from "../../artifacts/ArtifactReader.js";
 import { readStableArtifact } from "../../artifacts/readStableArtifact.js";
 import { normalizeArtifactPath } from "../../artifacts/ArtifactPaths.js";
@@ -55,7 +55,7 @@ export class LocalWebScriptArtifacts implements WebScriptArtifactPort {
          "path",
          `Selected source path changes during normalization: ${selected.content.relative_path}`,
        );
-      const root = dirname(input.manifest_path);
+      const root = resolve(dirname(input.manifest_path));
      const sourcePath = join(root, "files", portable);
      targetPath = sourcePath;
      await assertContained(root, sourcePath);
@@ -161,14 +161,28 @@ it("rejects identical duplicate core fields before schema validation", () => {
  expect(() => decodeHarCapture(text, [])).toThrow("duplicate");
 });

-it("reports an unsupported JSON schema boundary instead of dropping a producer property", () => {
+it("preserves prototype-named producer members through the capture boundary", () => {
  const text = JSON.stringify(historicalHar()).replace(
    '"cache":{}',
    '"cache":{},"_extension":{"__proto__":{"preserved":7},"constructor":"ordinary"}',
  );
-  expect(() => decodeHarCapture(text, [])).toThrow(
-    "JSON schema boundary cannot preserve",
-  );
+  const result = decodeHarCapture(text, []);
+  const reported = result.records[0]?.reported;
+  expect(reported).toBeDefined();
+  if (
+    reported === undefined ||
+    reported === null ||
+    typeof reported !== "object" ||
+    Array.isArray(reported)
+  )
+    throw new Error("No HAR object record was retained");
+  const extension = reported["_extension"];
+  expect(extension).toEqual({
+    ["__proto__"]: { preserved: 7 },
+    constructor: "ordinary",
+  });
+  expect(Object.getPrototypeOf(extension)).toBe(Object.prototype);
+  expect(Reflect.get(Object.prototype, "preserved")).toBeUndefined();
 });

 it("preserves Unicode, offsets, sizes, duplicate URLs and opaque extensions without inventing bytes", () => {
@@ -58,11 +58,9 @@ export const parseHarJson = (text: string): unknown => {
        });
      },
      onObjectProperty: (key) => {
-        if (key === "__proto__")
-          throw new CaptureFormatError(
-            "unsupported",
-            "HAR object contains a __proto__ member that the current JSON schema boundary cannot preserve.",
-          );
+        // Prototype-named members are kept as ordinary own properties: the
+        // members map keys them without prototype setters, and
+        // Object.fromEntries materializes them as own data properties.
        const frame = frames.at(-1);
        if (frame?.kind !== "object")
          throw new TypeError(
@@ -4,6 +4,7 @@ import { Cli } from "incur";

 import { createLogger, parseLogLevel } from "./logger.js";
 import { PRODUCT_IDENTITY } from "./identity.js";
+import { npxRegistrationCommand } from "./application/ClientRegistrationIdentity.js";
 import { registerSetupCommands } from "./cli/setupCommands.js";
 import { registerCoreAnalysisCommands } from "./cli/coreAnalysisCommands.js";
 import { registerUtilityCommands } from "./cli/utilityCommands.js";
@@ -47,7 +48,7 @@ export const createCli = (
    version: PRODUCT_IDENTITY.packageVersion,
    description: "Reverse engineer anything from your terminal or agent.",
    mcp: {
-      command: PRODUCT_IDENTITY.mcpCommand,
+      command: npxRegistrationCommand().join(" "),
      instructions:
        "Ask what software, artifact, protocol, or behavior the user wants to understand, then choose the available investigation capabilities that can produce evidence.",
    },
@@ -12,7 +12,7 @@ export const WEB_NETWORK_CAPTURE_TOOL_CONTRACTS = [
    name: "inspect_web_network_capture",
    ...toolContractMetadata("inspect_web_network_capture"),
    description:
-      "Inspect retained local HAR 1.2 or native mitmproxy capture records without contacting recorded URLs. Returns original ordinals, pointers/byte ranges, preserved producer fields, precise numeric representations and exact exposed binary bytes inline. Excludes known transport credentials and explicitly marked values. Decodes every record before optional ordinal selection; malformed or oversized captures return no partial success. Duplicate HAR members are invalid; prototype-named __proto__ members are unsupported by the current shared JSON boundary. Uses pinned upstream parsers, owned temporary files and bounded offline processes. Native mitmproxy requires caller-supplied mitmdump 12.2.3 on Linux. Browser transaction IDs, runtime attribution and original bytes of HAR Unicode text remain unknown.",
+      "Inspect retained local HAR 1.2 or native mitmproxy capture records without contacting recorded URLs. Returns original ordinals, pointers/byte ranges, preserved producer fields, precise numeric representations and exact exposed binary bytes inline. Excludes known transport credentials and explicitly marked values. Decodes every record before optional ordinal selection; malformed or oversized captures return no partial success. Duplicate HAR members are invalid; prototype-named members such as __proto__ are preserved as ordinary own JSON members without prototype mutation. Uses pinned upstream parsers, owned temporary files and bounded offline processes. Native mitmproxy requires caller-supplied mitmdump 12.2.3 on Linux. Browser transaction IDs, runtime attribution and original bytes of HAR Unicode text remain unknown.",
    kind: "browser-provider",
    inputSchema: inspectWebNetworkCaptureInputSchema,
    outputSchema: evidenceResultOf(webNetworkCaptureSchema),
@@ -162,8 +162,7 @@ export const analysisErrorUserMessage = (error: AnalysisError): string => {
      : `Evidence ${error.evidenceId} does not match the requested reference (${error.reason}). Check the expected and actual identity in the diagnostic details.`;
  if (error instanceof EvidenceIntegrityError)
    return "Evidence is invalid or has changed. Recreate or re-import it, then try again.";
-  if (error instanceof EvidenceFileError)
-    return evidenceFileMessage(error.reason);
+  if (error instanceof EvidenceFileError) return evidenceFileMessage(error);
  if (error instanceof UnknownRegistryError && error.reason === "not-found")
    return "The requested residual unknown does not exist in this session. Check the unknown_id and try again.";
  if (error instanceof UnknownRegistryError)
@@ -258,7 +257,14 @@ const artifactMessage = (reason: ArtifactOperationError["reason"]): string => {
  return "Artifact could not be read or written. Check file access and try again.";
 };

-const evidenceFileMessage = (reason: EvidenceFileError["reason"]): string => {
+const evidenceFileMessage = ({
+  operation,
+  reason,
+}: EvidenceFileError): string => {
+  if (reason === "missing")
+    return operation === "read"
+      ? "Evidence file does not exist at the selected path. Check the path and try again."
+      : "Evidence output directory does not exist. Choose an existing directory and try again.";
  if (reason === "not-file")
    return "Evidence path does not point to a regular file. Choose a file and try again.";
  if (reason === "exists")
@@ -259,7 +259,11 @@ const artifactStateErrorDetails = (
    };
  if (error instanceof UnknownRegistryError) return { reason: error.reason };
  if (error instanceof EvidenceFileError)
-    return { operation: error.operation, reason: error.reason };
+    return {
+      operation: error.operation,
+      reason: error.reason,
+      ...(error.path === undefined ? {} : { path: error.path }),
+    };
  return undefined;
 };

@@ -1,4 +1,5 @@
 import { z } from "zod";
+import { AnalysisInputError } from "../analysisErrorCore.js";
 import { jsonValueSchema, type JsonValue } from "../jsonValue.js";

 /** Select one archive within the active bundle and optionally one named root. */
@@ -85,7 +86,14 @@ export const projectKeyedArchive = (
  if (top === undefined || Object.keys(top).length === 0)
    throw new TypeError("Keyed archive has no $top roots");
  if (selection.root !== undefined && !Object.hasOwn(top, selection.root))
-    throw new TypeError(`Archive root does not exist: ${selection.root}`);
+    throw new AnalysisInputError("inspect_keyed_archive", undefined, [
+      {
+        path: ["root"],
+        reason: "invalid_value",
+        message: `Archive root does not exist: ${selection.root}. Select one of the archive's $top roots or omit root.`,
+        expected: Object.keys(top),
+      },
+    ]);
  const roots =
    selection.root === undefined
      ? top
@@ -44,13 +44,27 @@ it("snapshots caller-owned payloads before deriving their identity", () => {
 });

 describe("analysis evidence identity", () => {
-  it("normalizes prototype-named parameter keys", () => {
+  it("preserves prototype-named parameter keys and their semantic identity", () => {
    const evidence = createEvidence(TARGET, PROVIDER, {
      operation: "health",
      parameters: Object.fromEntries([["__proto__", false]]),
      result: true,
    });
+    expect(evidence.parameters).toEqual({ ["__proto__"]: false });
+    expect(Object.hasOwn(evidence.parameters, "__proto__")).toBe(true);
    expect(parseEvidence(evidence)).toEqual(evidence);
+    const stripped = createEvidence(TARGET, PROVIDER, {
+      operation: "health",
+      parameters: {},
+      result: true,
+    });
+    expect(stripped.evidence_id).not.toBe(evidence.evidence_id);
+    expect(() =>
+      parseEvidence({
+        ...evidence,
+        parameters: { ["__proto__"]: true },
+      }),
+    ).toThrow(/semantic identifier/u);
  });

  it.prop([
@@ -280,3 +294,27 @@ describe("evidence parameter depth bound", () => {
    ).toBe(true);
  });
 });
+
+it("preserves prototype-named raw and normalized results with aligned identity", () => {
+  const result = { ["__proto__"]: { preserved: 7 }, constructor: "ordinary" };
+  const evidence = createEvidence(TARGET, PROVIDER, {
+    operation: "health",
+    parameters: {},
+    result,
+    rawResult: result,
+  });
+  const parsed = parseEvidence(evidence);
+  expect(parsed.normalized_result).toEqual(result);
+  expect(parsed.raw_result).toEqual(result);
+  expect(Object.getPrototypeOf(parsed.normalized_result)).toBe(
+    Object.prototype,
+  );
+  expect(Reflect.get(Object.prototype, "preserved")).toBeUndefined();
+  const stripped = createEvidence(TARGET, PROVIDER, {
+    operation: "health",
+    parameters: {},
+    result: { constructor: "ordinary" },
+    rawResult: { constructor: "ordinary" },
+  });
+  expect(stripped.evidence_id).not.toBe(evidence.evidence_id);
+});
@@ -7,7 +7,11 @@ import {
  type AnalysisProfileCommitment,
 } from "./analysisProfile.js";
 import type { BinaryTarget } from "./binaryTarget.js";
-import { jsonValueSchema, type JsonValue } from "./jsonValue.js";
+import {
+  jsonObjectSchema,
+  jsonValueSchema,
+  type JsonValue,
+} from "./jsonValue.js";
 import { digestSchema } from "./../domain/digests.js";
 import { prefixedDigestSchema } from "./../domain/digests.js";

@@ -89,7 +93,7 @@ const evidenceBaseSchema = z
    provider: providerSchema,
    predicate_type: z.string().min(1),
    operation: z.string().min(1),
-    parameters: z.record(z.string(), jsonValueSchema),
+    parameters: jsonObjectSchema,
    raw_result: jsonValueSchema.nullable(),
    normalized_result: jsonValueSchema,
    confidence: z.enum(["observed", "derived", "inferred"]),
@@ -182,6 +182,34 @@ const referencedEvidenceIds = (unknown: ResidualUnknown): readonly string[] => [
  ...(unknown.resolution?.evidence_ids ?? []),
 ];

+/**
+ * Name the bundle constraint that failed and how to recover. A single
+ * Evidence record, such as one command result, is not a bundle.
+ */
+export const describeEvidenceBundleFailure = (
+  input: unknown,
+  cause: unknown,
+): string => {
+  const record = evidenceRecordSchema.safeParse(input);
+  if (record.success)
+    return `Expected an Evidence bundle with records and manifest arrays, but this JSON is one Evidence record (${record.data.evidence_id}). Export a session bundle with the MCP export_evidence_bundle tool and supply that file.`;
+  return cause instanceof z.ZodError
+    ? `Evidence bundle does not match the bundle schema ${describeValidationFailure(cause)}. Supply an unmodified bundle written by export_evidence_bundle or rea evidence-export.`
+    : `Evidence bundle validation failed: ${describeValidationFailure(cause)}. Recreate or re-export the bundle, then try again.`;
+};
+
+/** Locate the first schema issue, or keep a thrown constraint message. */
+export const describeValidationFailure = (cause: unknown): string => {
+  if (!(cause instanceof z.ZodError))
+    return cause instanceof Error ? cause.message : String(cause);
+  const [first, ...rest] = cause.issues;
+  const location =
+    first === undefined || first.path.length === 0
+      ? "the document root"
+      : first.path.map(String).join(".");
+  return `at ${location}: ${first?.message ?? "invalid value"}${rest.length === 0 ? "" : ` (${String(rest.length)} more issues)`}`;
+};
+
 /** Parse records, verify semantic IDs, and reject inconsistent manifests. */
 export const parseEvidenceBundle = (input: unknown): EvidenceBundle => {
  const parsed = evidenceBundleSchema.parse(input);
@@ -1,8 +1,20 @@
-import { AnalysisError } from "./analysisErrorBase.js";
+import {
+  AnalysisError,
+  type AnalysisErrorOptions,
+} from "./analysisErrorBase.js";

 /** Evidence identity, schema, or bundle manifests failed integrity checks. */
 export class EvidenceIntegrityError extends AnalysisError {
  readonly _tag = "EvidenceIntegrityError";
+  override readonly userMessage: string | undefined;
+
+  constructor(
+    message: string,
+    options?: AnalysisErrorOptions & { readonly userMessage?: string },
+  ) {
+    super(message, options);
+    this.userMessage = options?.userMessage;
+  }
 }

 /** A session Evidence reference is missing or has the wrong semantic identity. */
@@ -25,11 +37,15 @@ export class EvidenceReferenceError extends EvidenceIntegrityError {
 export class EvidenceFileError extends AnalysisError {
  readonly _tag = "EvidenceFileError";

+  /** Caller-selected path that failed, resolved against the working directory. */
+  readonly path: string | undefined;
+
  constructor(
    readonly operation: "read" | "write",
-    readonly reason: "not-file" | "exists" | "invalid-json" | "io",
-    options?: ErrorOptions,
+    readonly reason: "not-file" | "exists" | "invalid-json" | "missing" | "io",
+    options?: ErrorOptions & { readonly path?: string },
  ) {
    super(`Evidence bundle ${operation} failed: ${reason}`, options);
+    this.path = options?.path;
  }
 }
@@ -12,16 +12,21 @@ import { digestSchema } from "../digests.js";
 import { prefixedDigestSchema } from "../digests.js";

 const semanticNodeIdSchema = prefixedDigestSchema("jsrg_node");
+const literalValueSchema = jsonValueSchema.refine(
+  (value) =>
+    value === null ||
+    typeof value === "string" ||
+    typeof value === "number" ||
+    typeof value === "boolean",
+  "Literal seeds accept only JSON primitive values",
+);
+// Zod derivations drop the shared schema's JSON Schema projection override;
+// re-apply it so MCP catalog generation keeps projecting `{}`.
+literalValueSchema._zod.toJSONSchema = () => ({});
+
 const literalSeedSchema = z.strictObject({
  kind: z.literal("literal"),
-  value: jsonValueSchema.refine(
-    (value) =>
-      value === null ||
-      typeof value === "string" ||
-      typeof value === "number" ||
-      typeof value === "boolean",
-    "Literal seeds accept only JSON primitive values",
-  ),
+  value: literalValueSchema,
 });

 /** Authenticated starting points accepted by semantic tracing. */
@@ -99,3 +99,34 @@ describe("jsonValueSchema depth bound", () => {
    ).toBe(true);
  });
 });
+
+it("preserves prototype-named members without prototype mutation", () => {
+  const input: unknown = JSON.parse(
+    '{"__proto__":{"preserved":7},"constructor":"ordinary","prototype":[1],"nested":{"\\u005f\\u005fproto\\u005f\\u005f":"escaped"},"list":[{"__proto__":null}]}',
+  );
+  const parsed = jsonObjectSchema.parse(input);
+  expect(parsed).toEqual(input);
+  expect(Object.getPrototypeOf(parsed)).toBe(Object.prototype);
+  expect(Object.hasOwn(parsed, "__proto__")).toBe(true);
+  expect(parsed["__proto__"]).toEqual({ preserved: 7 });
+  expect(parsed["constructor"]).toBe("ordinary");
+  expect(parsed["prototype"]).toEqual([1]);
+  expect(parsed["nested"]).toEqual({ ["__proto__"]: "escaped" });
+  expect(parsed["list"]).toEqual([{ ["__proto__"]: null }]);
+  expect(Object.getPrototypeOf(parsed["nested"])).toBe(Object.prototype);
+  expect(Reflect.get(Object.prototype, "preserved")).toBeUndefined();
+  expect(JSON.parse(JSON.stringify(parsed))).toEqual(input);
+});
+
+it.each([undefined, Number.NaN, Infinity, 1n, () => 0, new Date(0)])(
+  "rejects non-JSON values in prototype-named members (%s)",
+  (value) => {
+    for (const input of [
+      { ["__proto__"]: value },
+      { nested: [{ ["__proto__"]: value }] },
+    ]) {
+      expect(jsonValueSchema.safeParse(input).success).toBe(false);
+      expect(jsonObjectSchema.safeParse(input).success).toBe(false);
+    }
+  },
+);
@@ -1,67 +1,87 @@
 import { z } from "zod";

-/**
- * Maximum nesting depth accepted for JSON values.
- *
- * Sits well below the point where the recursive `z.json()` core overflows its
- * stack (measured between 2000 and 3000 on Node 24) while leaving room for
- * legitimately deep target-derived trees such as compiled NIB view hierarchies.
- */
+/** Maximum JSON nesting accepted before recursive result cloning. */
 export const MAX_JSON_DEPTH = 1000;

+/** JSON-safe value shared by domain, application, and adapter boundaries. */
+export type JsonValue =
+  | string
+  | number
+  | boolean
+  | null
+  | JsonValue[]
+  | { [key: string]: JsonValue };
+
 const isRecord = (value: unknown): value is Record<string, unknown> =>
  typeof value === "object" && value !== null && !Array.isArray(value);
+const recordShape = z.record(z.string(), z.unknown());

-const exceedsMaxDepth = (root: unknown): boolean => {
-  // Depth counts edges from the root.
+const jsonValidationIssue = (root: unknown): string | undefined => {
  const pending: { value: unknown; depth: number }[] = [
    { value: root, depth: 0 },
  ];
  while (pending.length > 0) {
    const item = pending.pop();
    if (item === undefined) break;
-    if (item.depth > MAX_JSON_DEPTH) return true;
+    if (item.depth > MAX_JSON_DEPTH)
+      return `JSON value exceeds maximum nesting depth of ${MAX_JSON_DEPTH}`;
    const value = item.value;
-    if (Array.isArray(value)) {
+    if (
+      value === null ||
+      typeof value === "string" ||
+      typeof value === "boolean"
+    )
+      continue;
+    if (typeof value === "number") {
+      if (!Number.isFinite(value)) return "JSON numbers must be finite";
+    } else if (Array.isArray(value)) {
      for (const child of value)
        pending.push({ value: child, depth: item.depth + 1 });
-    } else if (isRecord(value)) {
-      for (const key of Object.keys(value))
-        pending.push({ value: value[key], depth: item.depth + 1 });
-    }
+    } else if (isRecord(value) && recordShape.safeParse(value).success) {
+      // Inspect every own member, including keys Zod's record parser skips.
+      for (const child of Object.values(value))
+        pending.push({ value: child, depth: item.depth + 1 });
+    } else return "Invalid JSON value";
  }
-  return false;
+  return undefined;
 };

-/**
- * JSON-safe value shared by domain, application, and adapter boundaries.
- *
- * An iterative depth guard runs before the recursive `z.json()` core so
- * hostile nested payloads surface as validation issues instead of RangeErrors.
- * The guard only refuses over-deep values; ordinary JSON parsing semantics
- * (including which members `z.json()` keeps) are unchanged.
- */
-const jsonCore = z.json();
-// Every JSON value satisfies `{}`. Advertise that instead of Zod's
-// self-referential `$defs` projection, which MCP clients and model APIs that
-// reject recursive JSON Schemas refuse. Runtime parsing still admits only JSON.
-// The override sits on the core as well as on the pipe because the standard
-// JSON Schema projection walks into pipe stages without consulting the outer
-// node, while the public toJSONSchema projection stops at the pipe.
-jsonCore._zod.toJSONSchema = () => ({});
+const preserveJsonValue = (value: JsonValue): JsonValue => {
+  if (Array.isArray(value)) return value.map(preserveJsonValue);
+  if (value !== null && typeof value === "object")
+    return Object.fromEntries<JsonValue>(
+      Object.entries(value).map(([key, child]) => [
+        key,
+        preserveJsonValue(child),
+      ]),
+    );
+  return value;
+};
+
+const validatedJsonValue = z.custom<JsonValue>(
+  (value) => jsonValidationIssue(value) === undefined,
+  {
+    error: (issue) => jsonValidationIssue(issue.input) ?? "Invalid JSON value",
+  },
+);
+// Keep both stages nonrecursive in public and Standard Schema projections.
+validatedJsonValue._zod.toJSONSchema = () => ({});
+
+/** Parse bounded JSON and retain all own data members without prototype setters. */
 export const jsonValueSchema = z
  .unknown()
-  .superRefine((value, context) => {
-    if (exceedsMaxDepth(value))
-      context.addIssue({
-        code: "custom",
-        message: `JSON value exceeds maximum nesting depth of ${MAX_JSON_DEPTH}`,
-      });
-  })
-  .pipe(jsonCore);
+  .nonoptional()
+  .pipe(validatedJsonValue)
+  .transform(preserveJsonValue);
 jsonValueSchema._zod.toJSONSchema = () => ({});

-/** JSON object boundary for caller-visible parameter maps. */
-export const jsonObjectSchema = z.record(z.string(), jsonValueSchema);
+const objectValidation = z.custom<Record<string, JsonValue>>(
+  isRecord,
+  "Expected JSON object",
+);
+const objectProjection = () => ({ type: "object", additionalProperties: {} });
+objectValidation._zod.toJSONSchema = objectProjection;

-export type JsonValue = z.infer<typeof jsonValueSchema>;
+/** JSON object boundary for caller-visible parameter maps. */
+export const jsonObjectSchema = jsonValueSchema.pipe(objectValidation);
+jsonObjectSchema._zod.toJSONSchema = objectProjection;
@@ -223,6 +223,10 @@ export interface UnverifiedProcessCapture {
  readonly cleanup: {
    readonly owned_process_group: "verified";
    readonly temporary_root: "removed";
+    /** Unrelated processes whose ownership token the host could not expose. */
+    readonly unverified_processes?:
+      | readonly UnverifiedCleanupProcess[]
+      | undefined;
  };
 }

@@ -232,10 +236,19 @@ const fileStateShape = {
  size: z.number().int().nonnegative(),
 };

+/** An unrelated process left untouched because its ownership is unknown. */
+export interface UnverifiedCleanupProcess {
+  readonly pid: number;
+  readonly reason: string;
+}
+
 /** A resource cleanup result retained when observations cannot be verified. */
 export interface ProcessCaptureResourceCleanup {
  readonly state: "cleaned" | "failed" | "unverified" | "not_required";
  readonly reason: string | null;
+  readonly unverified_processes?:
+    | readonly UnverifiedCleanupProcess[]
+    | undefined;
 }

 export interface ProcessCaptureCleanupReport {
@@ -348,6 +361,10 @@ const processSettlementSchema = z.discriminatedUnion("state", [
  }),
 ]);

+const unverifiedCleanupProcessesSchema = z.array(
+  z.strictObject({ pid: z.number().int().positive(), reason: z.string() }),
+);
+
 const processCaptureShapeSchema = z.strictObject({
  manifest: z.strictObject({
    rea_version: z.string().min(1),
@@ -478,12 +495,14 @@ const processCaptureShapeSchema = z.strictObject({
  cleanup: z.object({
    owned_process_group: z.literal("verified"),
    temporary_root: z.literal("removed"),
+    unverified_processes: unverifiedCleanupProcessesSchema.optional(),
  }),
 });

 const processCleanupResourceSchema = z.strictObject({
  state: z.enum(["cleaned", "failed", "unverified", "not_required"]),
  reason: z.string().nullable(),
+  unverified_processes: unverifiedCleanupProcessesSchema.optional(),
 });

 const partialObservationFieldSchema = <Schema extends z.ZodType>(
@@ -100,6 +100,7 @@ export const signatureVerification = (
  capture: NativeCommandCapture,
  path: string,
  unsigned: boolean,
+  progressCompleteness: "complete" | "ambiguous" = "complete",
 ): NonNullable<InspectSignature["verification"]> => {
  const lines = `${capture.stderr}\n${capture.stdout}`
    .split("\n")
@@ -109,11 +110,10 @@ export const signatureVerification = (
  );
  return {
    path,
-    status: verificationStatus(
-      capture,
-      codesignReasons(capture, path),
-      unsigned,
-    ),
+    status:
+      progressCompleteness === "ambiguous" && capture.exitCode !== 0
+        ? "unknown"
+        : verificationStatus(capture, codesignReasons(capture, path), unsigned),
    exit_code: capture.exitCode,
    diagnostics,
    prepared_nested_code: [
@@ -1,11 +1,11 @@
 import { expect, it } from "vitest";
-import { unconfirmedNestedCode } from "./NativeNestedCode.js";
+import { inspectNestedCodePaths } from "./NativeNestedCode.js";

 it("observes cancellation between nested filesystem lookups", async () => {
  const controller = new AbortController();
  const paths: string[] = [];
  await expect(
-    unconfirmedNestedCode(
+    inspectNestedCodePaths(
      {
        validated_nested_code: ["/app/first", "/app/second"],
      },
@@ -23,7 +23,7 @@ it("observes cancellation between nested filesystem lookups", async () => {
 });

 it("checks prepared-only fragments with the same completeness rules", async () => {
-  const warnings = await unconfirmedNestedCode(
+  const warnings = await inspectNestedCodePaths(
    { prepared_nested_code: ["/app/odd"], validated_nested_code: [] },
    undefined,
    {
@@ -33,9 +33,46 @@ it("checks prepared-only fragments with the same completeness rules", async () =
      names: async () => [],
    },
  );
-  expect(warnings).toContainEqual(
+  expect(warnings.limitations).toContainEqual(
    expect.stringContaining(
      'prepared nested code at "/app/odd", which does not exist',
    ),
  );
 });
+
+it.each(["EIO", "ESTALE"])(
+  "keeps observed records when path lookup fails with %s",
+  async (code) => {
+    const result = await inspectNestedCodePaths(
+      {
+        prepared_nested_code: ["/app/first"],
+        validated_nested_code: ["/app/second"],
+      },
+      undefined,
+      {
+        lookup: async () => {
+          throw Object.assign(new Error("lookup failed"), { code });
+        },
+        names: async () => [],
+      },
+    );
+    expect(result.limitations).toHaveLength(2);
+    expect(result.limitations.every((message) => message.includes(code))).toBe(
+      true,
+    );
+    expect(result.progressAmbiguous).toBe(false);
+  },
+);
+it("detects newline ambiguity even when the reported first fragment does not exist", async () => {
+  const result = await inspectNestedCodePaths(
+    { prepared_nested_code: ["/app/odd"], validated_nested_code: [] },
+    undefined,
+    {
+      lookup: async () => {
+        throw Object.assign(new Error("missing"), { code: "ENOENT" });
+      },
+      names: async () => ["odd\n/app: invalid signature"],
+    },
+  );
+  expect(result.progressAmbiguous).toBe(true);
+});
@@ -1,5 +1,5 @@
 import { lstat, readdir } from "node:fs/promises";
-import { dirname } from "node:path";
+import { dirname, basename } from "node:path";

 /** Filesystem seam for path-completeness checks and cancellation regressions. */
 export interface NativeNestedPathView {
@@ -17,18 +17,25 @@ const FILE_SYSTEM: NativeNestedPathView = {
 const errorCode = (cause: unknown) =>
  cause instanceof Error && "code" in cause ? cause.code : undefined;

-/** Preserve reported paths, but qualify missing, denied or newline-ambiguous records. */
-export const unconfirmedNestedCode = async (
+/** Completeness of newline-delimited progress records, distinct from verification. */
+export interface NestedCodePathInspection {
+  readonly limitations: readonly string[];
+  readonly progressAmbiguous: boolean;
+}
+
+/** Preserve reported paths and operational errors, and identify ambiguous progress. */
+export const inspectNestedCodePaths = async (
  verification: {
    readonly validated_nested_code: readonly string[];
    readonly prepared_nested_code?: readonly string[];
  },
  signal?: AbortSignal,
  view: NativeNestedPathView = FILE_SYSTEM,
-): Promise<string[]> => {
+): Promise<NestedCodePathInspection> => {
  signal?.throwIfAborted();
  const limitations: string[] = [];
-  const directories = new Map<string, Promise<boolean>>();
+  const directories = new Map<string, Promise<ReadonlySet<string>>>();
+  let progressAmbiguous = false;
  const records = new Map<string, "prepared" | "validated">();
  for (const path of verification.prepared_nested_code ?? [])
    records.set(path, "prepared");
@@ -47,11 +54,14 @@ export const unconfirmedNestedCode = async (
        );
        continue;
      }
-      if (code !== "ENOENT" && code !== "ENOTDIR") throw cause;
-      limitations.push(
-        `codesign reported ${record} nested code at ${JSON.stringify(path)}, which does not exist; a nested path probably contains a newline, so structured nested-code records and diagnostics may hold fragments of it.`,
-      );
-      continue;
+      if (code === "ENOENT" || code === "ENOTDIR")
+        limitations.push(
+          `codesign reported ${record} nested code at ${JSON.stringify(path)}, which does not exist; structured nested-code records may hold fragments of a path containing a newline.`,
+        );
+      else
+        limitations.push(
+          `Could not confirm completeness of codesign nested path ${JSON.stringify(path)}: ${cause instanceof Error ? cause.message : String(cause)} (${String(code ?? "unknown")}); the reported path may be a fragment.`,
+        );
    }
    signal?.throwIfAborted();
    const parent = dirname(path);
@@ -59,24 +69,33 @@ export const unconfirmedNestedCode = async (
    if (names === undefined) {
      names = view
        .names(parent)
-        .then((entries) => entries.some((name) => name.includes("\n")));
+        .then(
+          (entries) =>
+            new Set(
+              entries
+                .filter((name) => name.includes("\n"))
+                .map((name) => name.slice(0, name.indexOf("\n"))),
+            ),
+        );
      directories.set(parent, names);
    }
    try {
-      const ambiguous = await names;
+      const prefixes = await names;
+      const ambiguous = prefixes.has(basename(path));
      signal?.throwIfAborted();
-      if (ambiguous)
+      if (ambiguous) {
+        progressAmbiguous = true;
        limitations.push(
-          `codesign reported ${record} nested code at ${JSON.stringify(path)}, which exists but could be the first line of a nested path containing a newline; structured nested-code records are ambiguous and should not be trusted as complete.`,
+          `codesign reported ${record} nested code at ${JSON.stringify(path)}, which could be the first line of a nested path containing a newline; structured nested-code records are ambiguous and should not be trusted as complete.`,
        );
+      }
    } catch (cause: unknown) {
      signal?.throwIfAborted();
-      if (!(cause instanceof Error) || !("code" in cause)) throw cause;
      limitations.push(
-        `Could not confirm completeness of codesign nested path ${JSON.stringify(path)} from parent directory ${JSON.stringify(parent)}: ${cause.message}`,
+        `Could not confirm completeness of codesign nested path ${JSON.stringify(path)} from parent directory ${JSON.stringify(parent)}: ${cause instanceof Error ? cause.message : String(cause)}`,
      );
    }
  }
  signal?.throwIfAborted();
-  return limitations;
+  return { limitations, progressAmbiguous };
 };
@@ -37,7 +37,7 @@ import {
  signedCodePath,
  stapledTicket,
 } from "./NativeSignaturePosture.js";
-import { unconfirmedNestedCode } from "./NativeNestedCode.js";
+import { inspectNestedCodePaths } from "./NativeNestedCode.js";

 interface SignatureDisplays {
  readonly display: NativeCommandCapture;
@@ -71,6 +71,15 @@ const signatureDisplays = async (
          NATIVE_MACOS_PROVIDER_IDENTITY.id,
          "inspect_signature",
          {
+            diagnostics: {
+              path,
+              tool: result.tool,
+              arguments: [...result.arguments],
+              exit_code: result.exitCode,
+              signal: result.signal,
+              raw_stdout: result.stdout,
+              raw_stderr: result.stderr,
+            },
            cause: new NativeCommandFailure(
              "codesign",
              "nonzero-exit",
@@ -127,10 +136,10 @@ export const inspectNativeSignature = async (options: {
    captures.push(anchor.value);
    appleOrigin = anchor.value.exitCode === 0;
    if (!appleOrigin) {
-      const reason = codesignReasons(anchor.value, code).find(
-        (line) => line.trim().length > 0,
-      );
-      appleOriginFailure = reason ?? `codesign exited ${anchor.value.exitCode}`;
+      const reason = codesignReasons(anchor.value, code)
+        .filter((line) => line.trim().length > 0)
+        .join("\n");
+      appleOriginFailure = reason || `codesign exited ${anchor.value.exitCode}`;
    }
  }
  const slices = await inspectSignatureSlices(
@@ -145,16 +154,28 @@ export const inspectNativeSignature = async (options: {
    slices.value.signed === undefined ? unsigned : !slices.value.signed;
  // Verification is independent evidence: uncertain display probes must not
  // erase an explicit signature failure from the verifier.
-  const verification = signatureVerification(
+  const reportedVerification = signatureVerification(
    verified.value,
    code,
    aggregateUnsigned,
  );
+  const nestedPaths = await inspectNestedCodePaths(
+    reportedVerification,
+    signal,
+  );
+  const verification = nestedPaths.progressAmbiguous
+    ? signatureVerification(
+        verified.value,
+        code,
+        aggregateUnsigned,
+        "ambiguous",
+      )
+    : reportedVerification;
  const limitations = [
    ...parsed.limitations,
    ...SIGNATURE_POSTURE_LIMITATIONS,
    ...slices.value.limitations,
-    ...(await unconfirmedNestedCode(verification, signal)),
+    ...nestedPaths.limitations,
  ];
  if (entitlementValue.omittedPrototypeKeys !== 0)
    limitations.push(
@@ -24,3 +24,16 @@ it("rejects empty, arbitrary, truncated and contradictory ticket containers", as
  ticket.writeUInt32LE(2, 16 + 4 + 8);
  expect(await inspect(ticket)).toContain("hash records disagree");
 });
+
+it("requires the complete signature field and validates all padding bytes", async () => {
+  const bytes = Buffer.from(notarizationTicketFixture());
+  expect(await inspect(bytes.subarray(0, bytes.length - 64))).toContain(
+    "72 bytes",
+  );
+  expect(await inspect(bytes)).toBeNull();
+  bytes[bytes.length - 1] = 1;
+  expect(await inspect(bytes)).toContain("signature padding");
+  expect(await inspect(Buffer.concat([bytes, Buffer.alloc(1)]))).toContain(
+    "72 bytes",
+  );
+});
@@ -6,7 +6,7 @@ export type TicketReadAt = (

 /**
 * Inspect the local s8ch/g8tk ticket framing. Observed in stapled app tickets;
- * see bytewitch's NotarizedTicket decoder and apple-platform-rs ticket_lookup.
+ * see https://www.mothersruin.com/software/Archaeology/reverse/tickets.html.
 * This does not authenticate certificates, signatures, or notarized cdhashes.
 */
 export const ticketStructureIssue = async (
@@ -38,16 +38,18 @@ export const ticketStructureIssue = async (
  const certificates = await derSequenceExtent(read, 16, certificateSize);
  if (certificates !== certificateSize)
    return "Ticket certificate block has malformed DER framing";
+  const signatureFieldSize = 72;
+  if (size - signatureOffset !== signatureFieldSize)
+    return "Ticket signature field is truncated or does not contain exactly 72 bytes";
  const signatureSize = await derSequenceExtent(
    read,
    signatureOffset,
-    size - signatureOffset,
+    signatureFieldSize,
  );
  if (signatureSize === null || signatureSize < 8)
    return "Ticket signature has malformed DER framing";
-  // ECDSA encodings can be padded to 72 bytes; only zero padding is accepted.
+  // The fixed signature field contains DER followed by zero padding.
  const paddingSize = size - signatureOffset - signatureSize;
-  if (paddingSize > 2) return "Ticket has unrecognized trailing bytes";
  const padding = await read(signatureOffset + signatureSize, paddingSize);
  if (padding.byteLength !== paddingSize || padding.some((byte) => byte !== 0))
    return "Ticket has malformed signature padding";
@@ -99,92 +99,102 @@ describe("capture-local process ownership", () => {
    expect(signalGroup).toHaveBeenCalledWith(process.processGroupId, "SIGKILL");
  });

-  it("cleans verified owners before reporting an unrelated opaque process", async () => {
-    const owned: ProcessTableEntry = {
-      pid: 905,
-      parentPid: 1,
-      processGroupId: 905,
-      state: "S",
-      command: "owned-detached-child",
-    };
-    const opaque: ProcessTableEntry = {
-      pid: 906,
-      parentPid: 1,
-      processGroupId: 906,
-      state: "S",
-      command: "unrelated-process",
-    };
-    const malformed: ProcessTableEntry = {
-      ...opaque,
-      pid: 907,
-      processGroupId: 907,
-      command: "malformed-procargs-process",
-    };
-    const sysctlDenied: ProcessTableEntry = {
-      ...opaque,
-      pid: 908,
-      processGroupId: 908,
-      command: "sysctl-denied-process",
-    };
-    const signalGroup = vi.fn();
-    const host: ProcessOwnershipHost = {
-      listProcesses: () =>
-        Promise.resolve([owned, opaque, malformed, sysctlDenied]),
-      environment: (pid) =>
-        pid === owned.pid
-          ? Promise.resolve({ REA_PROCESS_RUN_ID: "run-token" })
-          : Promise.reject(new Error("permission denied")),
-      runTokens: (entries) =>
-        Promise.resolve(
-          new Map(
-            entries.map(({ pid }) => [
-              pid,
-              pid === owned.pid
-                ? { state: "readable", runId: "run-token" as const }
-                : {
-                    state: "unavailable",
-                    reason:
-                      pid === malformed.pid
-                        ? ("malformed_procargs" as const)
-                        : pid === sysctlDenied.pid
-                          ? ("sysctl_failed_1" as const)
-                          : ("environment_unavailable" as const),
-                  },
-            ]),
+  it.skipIf(typeof process.getuid !== "function")(
+    "cleans verified owners and records unrelated opaque candidates as unverified",
+    async () => {
+      const owned: ProcessTableEntry = {
+        pid: 905,
+        parentPid: 1,
+        processGroupId: 905,
+        state: "S",
+        command: "owned-detached-child",
+      };
+      const opaque: ProcessTableEntry = {
+        pid: 906,
+        parentPid: 1,
+        processGroupId: 906,
+        state: "S",
+        command: "/usr/bin/unrelated-process",
+      };
+      const malformed: ProcessTableEntry = {
+        ...opaque,
+        pid: 907,
+        processGroupId: 907,
+        uid: process.getuid?.() === 0 ? 1 : 0,
+        command: "/usr/bin/malformed-procargs-process",
+      };
+      const sysctlDenied: ProcessTableEntry = {
+        ...opaque,
+        pid: 908,
+        processGroupId: 908,
+        uid: process.getuid?.() === 0 ? 1 : 0,
+        command: "/usr/bin/sysctl-denied-process",
+      };
+      const signalGroup = vi.fn();
+      const host: ProcessOwnershipHost = {
+        platform: "darwin",
+        listProcesses: () =>
+          Promise.resolve([owned, opaque, malformed, sysctlDenied]),
+        environment: (pid) =>
+          pid === owned.pid
+            ? Promise.resolve({ REA_PROCESS_RUN_ID: "run-token" })
+            : Promise.reject(new Error("permission denied")),
+        runTokens: (entries) =>
+          Promise.resolve(
+            new Map(
+              entries.map(({ pid }) => [
+                pid,
+                pid === owned.pid
+                  ? { state: "readable", runId: "run-token" as const }
+                  : {
+                      state: "unavailable",
+                      reason:
+                        pid === malformed.pid
+                          ? ("malformed_procargs" as const)
+                          : pid === sysctlDenied.pid
+                            ? ("sysctl_failed_1" as const)
+                            : ("platform_binary_environment_withheld" as const),
+                    },
+              ]),
+            ),
          ),
-        ),
-      signalGroup,
-    };
+        signalGroup,
+      };

-    await expect(
-      cleanupOwnedProcessGroup(
-        {
-          runId: "run-token",
-          leaderPid: 100,
-          processGroupId: 100,
-          sweepTokenOwnedProcesses: true,
-        },
-        host,
-      ),
-    ).resolves.toMatchObject({
-      cleaned: false,
-      reason:
-        "process ownership token could not be read for 3 live process(es): environment_unavailable=1, malformed_procargs=1, sysctl_errno_1=1",
-    });
-    expect(signalGroup).toHaveBeenCalledWith(owned.processGroupId, "SIGKILL");
-    expect(signalGroup).not.toHaveBeenCalledWith(
-      opaque.processGroupId,
-      "SIGKILL",
-    );
-    expect(signalGroup).not.toHaveBeenCalledWith(
-      malformed.processGroupId,
-      "SIGKILL",
-    );
-    expect(signalGroup).not.toHaveBeenCalledWith(
-      sysctlDenied.processGroupId,
-      "SIGKILL",
-    );
-  });
+      await expect(
+        cleanupOwnedProcessGroup(
+          {
+            runId: "run-token",
+            leaderPid: 100,
+            processGroupId: 100,
+            sweepTokenOwnedProcesses: true,
+          },
+          host,
+        ),
+      ).resolves.toMatchObject({
+        cleaned: true,
+        signaled: true,
+        unverified: [
+          { pid: 906, diagnostic: "platform_binary_environment_withheld" },
+          { pid: 907, diagnostic: "malformed_procargs" },
+          { pid: 908, diagnostic: "sysctl_failed_1" },
+        ],
+      });
+      expect(signalGroup).toHaveBeenCalledWith(owned.processGroupId, "SIGKILL");
+      expect(signalGroup).not.toHaveBeenCalledWith(
+        opaque.processGroupId,
+        "SIGKILL",
+      );
+      expect(signalGroup).not.toHaveBeenCalledWith(
+        malformed.processGroupId,
+        "SIGKILL",
+      );
+      expect(signalGroup).not.toHaveBeenCalledWith(
+        sysctlDenied.processGroupId,
+        "SIGKILL",
+      );
+    },
+  );
 });

 describe("capture-local process identity baselines", () => {
@@ -214,4 +214,38 @@ describe("process environment permission diagnostics", () => {
      expect(signalGroup).not.toHaveBeenCalled();
    },
  );
+
+  it.skipIf(typeof process.getuid !== "function")(
+    "records a foreign-uid unreadable candidate as unverified without signaling",
+    async () => {
+      const foreignUid = process.getuid?.() === 0 ? 1 : 0;
+      const signalGroup = vi.fn();
+      const adapter: ProcessOwnershipHost = {
+        listProcesses: () =>
+          Promise.resolve([
+            {
+              pid: 900,
+              parentPid: 1,
+              processGroupId: 900,
+              uid: foreignUid,
+              state: "S",
+              command: "unverifiable-process",
+            },
+          ]),
+        environment: () => Promise.reject(new Error("EINVAL: sysctl failed")),
+        signalGroup,
+      };
+      await expect(
+        cleanupOwnedProcessGroup(
+          { ...ownership, sweepTokenOwnedProcesses: true },
+          adapter,
+        ),
+      ).resolves.toMatchObject({
+        cleaned: true,
+        signaled: false,
+        unverified: [{ pid: 900, diagnostic: "EINVAL: sysctl failed" }],
+      });
+      expect(signalGroup).not.toHaveBeenCalled();
+    },
+  );
 });
@@ -67,7 +67,7 @@ describe("owned process-group cleanup discovery", () => {
 });

 describe("opaque process neighbors during cleanup", () => {
-  it("cleans verified run-owned groups while reporting an opaque neighbor", async () => {
+  it("cleans verified run-owned groups and records a withheld unrelated neighbor", async () => {
    const processes = [
      { pid: 100, parentPid: 1, processGroupId: 100, command: "capture" },
      {
@@ -76,6 +76,71 @@ describe("opaque process neighbors during cleanup", () => {
        processGroupId: 200,
        command: "detached-child",
      },
+      {
+        pid: 900,
+        parentPid: 1,
+        processGroupId: 900,
+        command: "/usr/bin/opaque-neighbor",
+      },
+    ].map((process) => ({ ...process, state: "S" }));
+    const signalGroup = vi.fn();
+    const identities = new Map(
+      processes.map(({ pid }) => [
+        pid,
+        { state: "readable" as const, identity: `start-${String(pid)}` },
+      ]),
+    );
+    const adapter: ProcessOwnershipHost = {
+      platform: "darwin",
+      listProcesses: () => Promise.resolve(processes),
+      environment: (pid) =>
+        Promise.resolve({
+          REA_PROCESS_RUN_ID: pid === 900 ? "unowned" : "run-token",
+        }),
+      processIdentities: () => Promise.resolve(identities),
+      runTokens: (members) =>
+        Promise.resolve(
+          new Map(
+            members.map(({ pid }) => [
+              pid,
+              pid === 900
+                ? {
+                    state: "unavailable" as const,
+                    reason: "platform_binary_environment_withheld",
+                  }
+                : { state: "readable" as const, runId: "run-token" },
+            ]),
+          ),
+        ),
+      signalGroup,
+    };
+
+    const result = await cleanupOwnedProcessGroup(
+      {
+        ...ownership,
+        sweepTokenOwnedProcesses: true,
+        captureBaseline: [],
+      },
+      adapter,
+    );
+
+    expect(result).toMatchObject({
+      cleaned: true,
+      signaled: true,
+      unverified: [
+        { pid: 900, diagnostic: "platform_binary_environment_withheld" },
+      ],
+    });
+    expect(signalGroup.mock.calls).toEqual([
+      [100, "SIGKILL"],
+      [200, "SIGKILL"],
+    ]);
+    expect(signalGroup).not.toHaveBeenCalledWith(900, "SIGKILL");
+  });
+
+  it("fails closed for an unrelated unreadable candidate the OS should expose", async () => {
+    const processes = [
+      { pid: 100, parentPid: 1, processGroupId: 100, command: "capture" },
      {
        pid: 900,
        parentPid: 1,
@@ -91,6 +156,7 @@ describe("opaque process neighbors during cleanup", () => {
      ]),
    );
    const adapter: ProcessOwnershipHost = {
+      platform: "darwin",
      listProcesses: () => Promise.resolve(processes),
      environment: (pid) =>
        Promise.resolve({
@@ -127,14 +193,83 @@ describe("opaque process neighbors during cleanup", () => {
      cleaned: false,
      reason: expect.stringContaining("environment_unavailable=1"),
    });
-    expect(signalGroup.mock.calls).toEqual([
-      [100, "SIGKILL"],
-      [200, "SIGKILL"],
-    ]);
+    expect(signalGroup.mock.calls).toEqual([[100, "SIGKILL"]]);
    expect(signalGroup).not.toHaveBeenCalledWith(900, "SIGKILL");
  });
 });

+describe("related sweep candidates during cleanup", () => {
+  it.each(["environment_unavailable", "platform_binary_environment_withheld"])(
+    "fails closed for a related candidate with %s",
+    async (diagnostic) => {
+      const processes = [
+        {
+          pid: 100,
+          parentPid: 1,
+          processGroupId: 100,
+          state: "S",
+          command: "capture",
+        },
+        {
+          pid: 101,
+          parentPid: 100,
+          processGroupId: 100,
+          state: "S",
+          uid: process.getuid?.() === 0 ? 1 : 0,
+          command: "ready-hang",
+        },
+      ];
+      const signalGroup = vi.fn();
+      const identities = new Map(
+        processes.map(({ pid }) => [
+          pid,
+          { state: "readable" as const, identity: `start-${String(pid)}` },
+        ]),
+      );
+      const adapter: ProcessOwnershipHost = {
+        listProcesses: () => Promise.resolve(processes),
+        environment: (pid) =>
+          pid === 100
+            ? Promise.resolve({ REA_PROCESS_RUN_ID: "run-token" })
+            : Promise.reject(new Error("EACCES: permission denied")),
+        processIdentities: () => Promise.resolve(identities),
+        runTokens: (members) =>
+          Promise.resolve(
+            new Map(
+              members.map(({ pid }) => [
+                pid,
+                pid === 100
+                  ? { state: "readable" as const, runId: "run-token" }
+                  : {
+                      state: "unavailable" as const,
+                      reason: diagnostic,
+                    },
+              ]),
+            ),
+          ),
+        signalGroup,
+      };
+
+      const result = await cleanupOwnedProcessGroup(
+        {
+          ...ownership,
+          sweepTokenOwnedProcesses: true,
+          captureBaseline: [],
+        },
+        adapter,
+      );
+
+      expect(result).toMatchObject({
+        cleaned: false,
+        reason: expect.stringContaining(
+          "process ownership token could not be read",
+        ),
+      });
+      expect(signalGroup).not.toHaveBeenCalled();
+    },
+  );
+});
+
 describe("sampled detached process groups during cleanup", () => {
  it("signals only token-authenticated sampled groups and reports an unowned sample", async () => {
    const processes = [
@@ -41,6 +41,8 @@ export interface ProcessTableEntry {
  readonly pid: number;
  readonly parentPid: number;
  readonly processGroupId: number;
+  /** Effective owner when the process table reports it. */
+  readonly uid?: number;
  readonly state: string;
  readonly command: string;
 }
@@ -123,9 +125,33 @@ interface ProcessOwnershipValidationFailure {
  readonly diagnostic?: string;
 }

+/**
+ * One live process the ownership sweep could not attribute or exonerate.
+ * Recorded as evidence instead of failing the capture: the process is not
+ * related to the owned tree, so cleanup cannot act on it and the operating
+ * system withheld or removed its token (for example, macOS strips the
+ * environment of Apple platform binaries, and foreign-uid processes return
+ * EINVAL for KERN_PROCARGS2).
+ */
+export interface OwnershipSweepUnverifiedProcess {
+  readonly pid: number;
+  readonly diagnostic: string;
+}
+
+/** Capture-owned process structures used to classify sweep candidates. */
+export interface OwnershipSweepRelation {
+  readonly leaderPid: number;
+  readonly processGroupId: number;
+  readonly sampledProcessGroupIds?: readonly number[];
+}
+
 /** Cleanup outcome with per-member diagnostics when ownership is uncertain. */
 export type ProcessCleanupResult =
-  | { readonly cleaned: true; readonly signaled: boolean }
+  | {
+      readonly cleaned: true;
+      readonly signaled: boolean;
+      readonly unverified?: readonly OwnershipSweepUnverifiedProcess[];
+    }
  | {
      readonly cleaned: false;
      readonly reason: string;
@@ -137,6 +163,7 @@ export type ProcessCleanupResult =
          | "process-identity-unavailable";
        readonly diagnostic?: string;
      }[];
+      readonly unverified?: readonly OwnershipSweepUnverifiedProcess[];
    };

 /** Token-verified liveness result used by post-root-exit settlement. */
@@ -242,8 +269,12 @@ export const cleanupOwnedProcessGroup = async (
    }
  }
  if (plan.unresolved.length > 0)
-    return cleanupValidationFailure(plan.unresolved);
-  return { cleaned: true, signaled };
+    return cleanupValidationFailure(plan.unresolved, plan.unverified);
+  return {
+    cleaned: true,
+    signaled,
+    ...(plan.unverified.length === 0 ? {} : { unverified: plan.unverified }),
+  };
 };

 /** Verify that no live process still carries an owned capture run token. */
@@ -251,6 +282,7 @@ export const verifyNoTokenOwnedProcesses = async (
  runId: string,
  host: ProcessOwnershipHost = systemHost,
  captureBaseline?: ProcessOwnershipBaseline,
+  relation?: OwnershipSweepRelation,
 ): Promise<ProcessCleanupResult> => {
  const processTable = await readLiveProcessTable(host);
  if (!processTable.available)
@@ -263,11 +295,21 @@ export const verifyNoTokenOwnedProcesses = async (
    runId,
    host,
    captureBaseline,
+    relation,
  );
-  if (scan.failures.length > 0) return cleanupValidationFailure(scan.failures);
-  return scan.owned.length === 0
-    ? { cleaned: true, signaled: false }
-    : { cleaned: false, reason: "token-owned process remained after cleanup" };
+  if (scan.failures.length > 0)
+    return cleanupValidationFailure(scan.failures, scan.unverified);
+  if (scan.owned.length > 0)
+    return {
+      cleaned: false,
+      reason: "token-owned process remained after cleanup",
+      ...(scan.unverified.length === 0 ? {} : { unverified: scan.unverified }),
+    };
+  return {
+    cleaned: true,
+    signaled: false,
+    ...(scan.unverified.length === 0 ? {} : { unverified: scan.unverified }),
+  };
 };

 const readLiveProcessTable = async (
@@ -293,6 +335,7 @@ interface OwnedCleanupPlan {
  readonly signalOrder: readonly number[];
  readonly tokenOwnedIdentities: ReadonlyMap<number, string | null>;
  readonly unresolved: readonly ProcessOwnershipValidationFailure[];
+  readonly unverified: readonly OwnershipSweepUnverifiedProcess[];
 }

 const createOwnedCleanupPlan = async (
@@ -313,8 +356,15 @@ const createOwnedCleanupPlan = async (
          ownership.runId,
          host,
          ownership.captureBaseline,
+          {
+            leaderPid: ownership.leaderPid,
+            processGroupId: ownership.processGroupId,
+            ...(sampledProcessGroupIds.size === 0
+              ? {}
+              : { sampledProcessGroupIds: [...sampledProcessGroupIds] }),
+          },
        )
-      : { owned: [], failures: [], identities: new Map() };
+      : { owned: [], failures: [], unverified: [], identities: new Map() };
  const tokenOwnedGroupIds = new Set(
    tokenOwned.owned.map(({ processGroupId }) => processGroupId),
  );
@@ -335,8 +385,15 @@ const createOwnedCleanupPlan = async (
          signalOrder: [],
          tokenOwnedIdentities: tokenOwned.identities,
          unresolved: tokenOwned.failures,
+          unverified: tokenOwned.unverified,
        }
-      : { cleaned: true, signaled: false };
+      : {
+          cleaned: true,
+          signaled: false,
+          ...(tokenOwned.unverified.length === 0
+            ? {}
+            : { unverified: tokenOwned.unverified }),
+        };
  let descendants: readonly ProcessTableEntry[] = [];
  if (launcher !== undefined) {
    const identityFailure = launcherIdentityFailure(launcher, ownership);
@@ -413,7 +470,7 @@ const createOwnedCleanupPlan = async (
      signalableGroups.add(processGroupId);
  }
  if (ownership.sweepTokenOwnedProcesses !== true && unresolved.length > 0)
-    return cleanupValidationFailure(unresolved);
+    return cleanupValidationFailure(unresolved, tokenOwned.unverified);
  return {
    signalOrder: [...signalableGroups]
      .filter((groupId) => processGroupIds.has(groupId))
@@ -426,6 +483,7 @@ const createOwnedCleanupPlan = async (
      ),
    tokenOwnedIdentities: tokenOwned.identities,
    unresolved,
+    unverified: tokenOwned.unverified,
  };
 };

@@ -478,7 +536,9 @@ const revalidateOwnedProcessGroup = async (

 const cleanupValidationFailure = (
  failures: readonly ProcessOwnershipValidationFailure[],
+  unverified: readonly OwnershipSweepUnverifiedProcess[] = [],
 ): ProcessCleanupResult => {
+  const unverifiedEntry = unverified.length === 0 ? {} : { unverified };
  const unreadable = failures.filter(
    ({ reason }) => reason === "environment-unreadable",
  );
@@ -487,12 +547,14 @@ const cleanupValidationFailure = (
      cleaned: false,
      reason: "process tree contains an unowned or PID-reused process",
      failures,
+      ...unverifiedEntry,
    };
  if (failures.some(({ reason }) => reason === "process-identity-unavailable"))
    return {
      cleaned: false,
      reason: "process identity could not be revalidated",
      failures,
+      ...unverifiedEntry,
    };
  if (unreadable.length > 0) {
    const counts = new Map<string, number>();
@@ -508,17 +570,20 @@ const cleanupValidationFailure = (
      cleaned: false,
      reason: `process ownership token could not be read for ${String(unreadable.length)} live process(es): ${breakdown}`,
      failures,
+      ...unverifiedEntry,
    };
  }
  return {
    cleaned: false,
    reason: "process ownership could not be revalidated",
    failures,
+    ...unverifiedEntry,
  };
 };

 const sanitizedTokenReadFailure = (diagnostic: string | undefined): string => {
  if (diagnostic === "environment_unavailable") return diagnostic;
+  if (diagnostic === "platform_binary_environment_withheld") return diagnostic;
  const environmentErrno = /^(EACCES|EPERM|ENOENT|ESRCH):/u.exec(
    diagnostic ?? "",
  );
@@ -630,14 +695,50 @@ const processOwnershipFailures = async (
 interface TokenOwnedProcessScan {
  readonly owned: readonly ProcessTableEntry[];
  readonly failures: readonly ProcessOwnershipValidationFailure[];
+  readonly unverified: readonly OwnershipSweepUnverifiedProcess[];
  readonly identities: ReadonlyMap<number, string | null>;
 }

+/** One sweep candidate whose run token could not be read. */
+interface UnreadableTokenCandidate {
+  readonly process: ProcessTableEntry;
+  readonly diagnostic: string;
+}
+
+const TOKEN_READ_RETRY_ATTEMPTS = 3;
+const TOKEN_READ_RETRY_DELAY_MS = 40;
+
+/** Darwin reports this when the kernel withholds a platform binary's environment. */
+const PLATFORM_BINARY_ENVIRONMENT_WITHHELD =
+  "platform_binary_environment_withheld";
+
+const currentProcessUid = (): number | undefined =>
+  typeof process.getuid === "function" ? process.getuid() : undefined;
+
+/**
+ * Whether the operating system provably withheld this candidate's run token:
+ * current macOS omits the environment of Apple platform binaries from
+ * KERN_PROCARGS2 and fails with EINVAL for processes owned by another
+ * account, and neither class can be token-verified by any caller. Such a
+ * candidate is recorded as unverified instead of failing an otherwise clean
+ * capture; every other unreadable candidate stays fail-closed.
+ */
+const environmentWithheldFromInspection = (
+  entry: ProcessTableEntry,
+  diagnostic: string,
+): boolean => {
+  const uid = currentProcessUid();
+  if (uid !== undefined && entry.uid !== undefined && entry.uid !== uid)
+    return true;
+  return diagnostic === PLATFORM_BINARY_ENVIRONMENT_WITHHELD;
+};
+
 const scanTokenOwnedProcesses = async (
  processes: readonly ProcessTableEntry[],
  runId: string,
  host: ProcessOwnershipHost,
  captureBaseline?: ProcessOwnershipBaseline,
+  relation?: OwnershipSweepRelation,
 ): Promise<TokenOwnedProcessScan> => {
  let candidates = processes;
  let candidateIdentities: ReadonlyMap<number, ProcessIdentityObservation> =
@@ -678,61 +779,98 @@ const scanTokenOwnedProcesses = async (
    }
    candidates = stableCandidates;
  }
+  const owned: ProcessTableEntry[] = [];
+  const ownedIdentities = new Map<number, string | null>();
+  const recordOwned = (process: ProcessTableEntry): void => {
+    owned.push(process);
+    const identity = candidateIdentities.get(process.pid);
+    ownedIdentities.set(
+      process.pid,
+      identity?.state === "readable" ? identity.identity : null,
+    );
+  };
  let bulkTokens: ReadonlyMap<number, ProcessRunTokenObservation> | undefined;
  if (host.runTokens !== undefined)
    bulkTokens = await host.runTokens(candidates);
-  const owned: ProcessTableEntry[] = [];
-  const ownedIdentities = new Map<number, string | null>();
+  const unreadable: UnreadableTokenCandidate[] = [];
  for (const process of candidates) {
    const bulkToken = bulkTokens?.get(process.pid);
    if (bulkToken !== undefined) {
      if (bulkToken.state === "readable") {
-        if (bulkToken.runId === runId) {
-          owned.push(process);
-          const identity = candidateIdentities.get(process.pid);
-          ownedIdentities.set(
-            process.pid,
-            identity?.state === "readable" ? identity.identity : null,
-          );
-        }
+        if (bulkToken.runId === runId) recordOwned(process);
        continue;
      }
-      if (!(await processIsGone(host, process.pid)))
-        failures.push({
-          pid: process.pid,
-          reason: "environment-unreadable",
-          diagnostic: bulkToken.reason,
-        });
+      unreadable.push({ process, diagnostic: bulkToken.reason });
      continue;
    }
    try {
-      if ((await host.environment(process.pid)).REA_PROCESS_RUN_ID === runId) {
-        owned.push(process);
-        const identity = candidateIdentities.get(process.pid);
-        ownedIdentities.set(
-          process.pid,
-          identity?.state === "readable" ? identity.identity : null,
-        );
-      }
+      if ((await host.environment(process.pid)).REA_PROCESS_RUN_ID === runId)
+        recordOwned(process);
    } catch (cause: unknown) {
-      try {
-        const live = liveProcesses(await host.listProcesses());
-        if (!live.some(({ pid }) => pid === process.pid)) continue;
-      } catch (recheckCause: unknown) {
-        failures.push({
-          pid: process.pid,
-          reason: "environment-unreadable",
-          diagnostic: `${errorMessage(cause)}; process liveness recheck failed: ${errorMessage(recheckCause)}`,
-        });
-        continue;
-      }
-      failures.push({
-        pid: process.pid,
-        reason: "environment-unreadable",
-        diagnostic: errorMessage(cause),
-      });
+      unreadable.push({ process, diagnostic: errorMessage(cause) });
    }
  }
+  const remaining = await settleUnreadableTokenCandidates(
+    unreadable,
+    runId,
+    host,
+    recordOwned,
+  );
+  const relatedPids = new Set<number>();
+  const relatedGroupIds = new Set<number>();
+  if (relation !== undefined) {
+    relatedPids.add(relation.leaderPid);
+    for (const descendant of descendantsOf(relation.leaderPid, processes))
+      relatedPids.add(descendant.pid);
+    relatedGroupIds.add(relation.processGroupId);
+    for (const processGroupId of relation.sampledProcessGroupIds ?? [])
+      if (Number.isSafeInteger(processGroupId) && processGroupId > 0)
+        relatedGroupIds.add(processGroupId);
+    for (const process of owned) relatedGroupIds.add(process.processGroupId);
+  }
+  const unverified: OwnershipSweepUnverifiedProcess[] = [];
+  const strict: UnreadableTokenCandidate[] = [];
+  const withheld: UnreadableTokenCandidate[] = [];
+  for (const candidate of remaining) {
+    const isRelated =
+      relation === undefined ||
+      relatedPids.has(candidate.process.pid) ||
+      relatedGroupIds.has(candidate.process.processGroupId);
+    if (
+      !isRelated &&
+      environmentWithheldFromInspection(candidate.process, candidate.diagnostic)
+    ) {
+      withheld.push(candidate);
+      continue;
+    }
+    strict.push(candidate);
+  }
+  let finalLive: ReadonlySet<number> | undefined;
+  try {
+    finalLive = new Set(
+      liveProcesses(await host.listProcesses()).map(({ pid }) => pid),
+    );
+  } catch (cause: unknown) {
+    void cause;
+    finalLive = undefined;
+  }
+  for (const candidate of strict) {
+    if (finalLive !== undefined && !finalLive.has(candidate.process.pid))
+      continue;
+    failures.push({
+      pid: candidate.process.pid,
+      reason: "environment-unreadable",
+      diagnostic: candidate.diagnostic,
+    });
+  }
+  for (const candidate of withheld) {
+    if (finalLive !== undefined && !finalLive.has(candidate.process.pid))
+      continue;
+    unverified.push({
+      pid: candidate.process.pid,
+      diagnostic: candidate.diagnostic,
+    });
+  }
  if (candidates.length > 0 && host.processIdentities !== undefined) {
    const afterRead = await host.processIdentities(candidates);
    const stillOwned: ProcessTableEntry[] = [];
@@ -756,9 +894,91 @@ const scanTokenOwnedProcesses = async (
          "process identity changed or became unavailable during token validation",
      });
    }
-    return { owned: stillOwned, failures, identities: ownedIdentities };
+    return {
+      owned: stillOwned,
+      failures,
+      unverified,
+      identities: ownedIdentities,
+    };
+  }
+  return { owned, failures, unverified, identities: ownedIdentities };
+};
+
+/**
+ * Re-read run tokens for unresolved sweep candidates so transient exec and
+ * exit states settle before classification. Each attempt revalidates
+ * liveness, refreshes the diagnostic, and is bounded by a fixed attempt
+ * budget; a still-unreadable candidate keeps its latest diagnostic.
+ */
+const settleUnreadableTokenCandidates = async (
+  pending: readonly UnreadableTokenCandidate[],
+  runId: string,
+  host: ProcessOwnershipHost,
+  recordOwned: (process: ProcessTableEntry) => void,
+): Promise<readonly UnreadableTokenCandidate[]> => {
+  let remaining = pending;
+  for (
+    let attempt = 0;
+    attempt < TOKEN_READ_RETRY_ATTEMPTS && remaining.length > 0;
+    attempt += 1
+  ) {
+    await new Promise<void>((resolve) =>
+      setTimeout(resolve, TOKEN_READ_RETRY_DELAY_MS),
+    );
+    let live: ReadonlySet<number> | undefined;
+    try {
+      live = new Set(
+        liveProcesses(await host.listProcesses()).map(({ pid }) => pid),
+      );
+    } catch (cause: unknown) {
+      void cause;
+      live = undefined;
+    }
+    let observations:
+      | ReadonlyMap<number, ProcessRunTokenObservation>
+      | undefined;
+    if (host.runTokens !== undefined) {
+      try {
+        observations = await host.runTokens(
+          remaining.map(({ process }) => process),
+        );
+      } catch (cause: unknown) {
+        void cause;
+        observations = undefined;
+      }
+    }
+    const stillUnreadable: UnreadableTokenCandidate[] = [];
+    for (const candidate of remaining) {
+      const pid = candidate.process.pid;
+      if (live !== undefined && !live.has(pid)) continue;
+      const observation =
+        observations?.get(pid) ?? (await readEnvironmentRunToken(host, pid));
+      if (observation.state === "readable") {
+        if (observation.runId === runId) recordOwned(candidate.process);
+        continue;
+      }
+      stillUnreadable.push({
+        process: candidate.process,
+        diagnostic: observation.reason,
+      });
+    }
+    remaining = stillUnreadable;
+  }
+  return remaining;
+};
+
+const readEnvironmentRunToken = async (
+  host: ProcessOwnershipHost,
+  pid: number,
+): Promise<ProcessRunTokenObservation> => {
+  try {
+    return {
+      state: "readable",
+      runId: (await host.environment(pid)).REA_PROCESS_RUN_ID,
+    };
+  } catch (cause: unknown) {
+    return { state: "unavailable", reason: errorMessage(cause) };
  }
-  return { owned, failures, identities: ownedIdentities };
 };

 const processIsGone = async (
@@ -192,19 +192,22 @@ export const createSystemProcessOwnershipHost = (
    if (platform === "win32") return [];
    const { stdout } = await execFileOutput(
      "ps",
-      ["-axo", "pid=,ppid=,pgid=,stat=,command="],
+      ["-axo", "pid=,ppid=,pgid=,uid=,stat=,command="],
      { env: hostEnvironment, ...(signal === undefined ? {} : { signal }) },
    );
    return stdout
      .split("\n")
-      .map((line) => /\s*(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(.*)/u.exec(line))
+      .map((line) =>
+        /\s*(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(.*)/u.exec(line),
+      )
      .filter((match): match is RegExpExecArray => match !== null)
      .map((match) => ({
        pid: Number(match[1]),
        parentPid: Number(match[2]),
        processGroupId: Number(match[3]),
-        state: match[4] ?? "",
-        command: match[5] ?? "",
+        uid: Number(match[4]),
+        state: match[5] ?? "",
+        command: match[6] ?? "",
      }));
  };
  const processIdentities: NonNullable<
@@ -704,10 +704,18 @@ export const releaseProcessResources = async (options: {
          "owned process cleanup is unverifiable on Windows without process-job authority",
      };
    } else {
+      const terminalPid = options.terminal.pid;
+      const relation = {
+        leaderPid: terminalPid,
+        processGroupId: terminalPid,
+        ...(options.sampledProcessGroupIds === undefined
+          ? {}
+          : { sampledProcessGroupIds: options.sampledProcessGroupIds }),
+      };
      const cleaned = await host.cleanupProcessGroup({
        runId: options.runId,
-        leaderPid: options.terminal.pid,
-        processGroupId: options.terminal.pid,
+        leaderPid: terminalPid,
+        processGroupId: terminalPid,
        sweepTokenOwnedProcesses: true,
        ...(options.sampledProcessGroupIds === undefined
          ? {}
@@ -716,6 +724,7 @@ export const releaseProcessResources = async (options: {
          ? {}
          : { captureBaseline: options.captureBaseline }),
      });
+      const unverified = [...(cleaned.unverified ?? [])];
      if (!cleaned.cleaned) {
        ownedProcessGroup = { state: "unverified", reason: cleaned.reason };
      } else {
@@ -724,11 +733,25 @@ export const releaseProcessResources = async (options: {
            options.runId,
            undefined,
            options.captureBaseline,
+            relation,
          ),
        );
+        unverified.push(...(verified.unverified ?? []));
        if (!verified.cleaned)
          ownedProcessGroup = { state: "unverified", reason: verified.reason };
      }
+      if (unverified.length > 0)
+        ownedProcessGroup = {
+          ...ownedProcessGroup,
+          unverified_processes: [
+            ...new Map(
+              unverified.map(({ pid, diagnostic }) => [
+                `${String(pid)}:${diagnostic}`,
+                { pid, reason: diagnostic },
+              ]),
+            ).values(),
+          ],
+        };
    }
  }
  let temporaryRoot: ProcessCaptureCleanupReport["temporary_root"] = {
@@ -892,7 +915,8 @@ export const resolveProcessResult = (
  }
  if (capture === undefined)
    throw new ProcessCaptureError("process capture produced no result");
-  if ("cleanup" in capture) return capture;
+  const unverifiedProcesses = cleanup.owned_process_group.unverified_processes;
+  if ("cleanup" in capture && unverifiedProcesses === undefined) return capture;

  const settlement: UnverifiedProcessCapture["settlement"] =
    capture.settlement.state === "quiesced"
@@ -902,9 +926,20 @@ export const resolveProcessResult = (
    return parseProcessCapture({
      ...capture,
      settlement,
+      residual_unknowns: [
+        ...capture.residual_unknowns,
+        ...(unverifiedProcesses ?? []).map(({ pid, reason }) => ({
+          scope: "process" as const,
+          reason: `Ownership of unrelated process ${String(pid)} could not be verified; it was left untouched: ${reason}`,
+        })),
+      ],
      cleanup: {
+        ...("cleanup" in capture ? capture.cleanup : {}),
        owned_process_group: "verified",
        temporary_root: "removed",
+        ...(unverifiedProcesses === undefined
+          ? {}
+          : { unverified_processes: unverifiedProcesses }),
      },
    });
  } catch (cause: unknown) {
@@ -142,6 +142,64 @@ it("waits for token-owned processes to exit after one cleanup signal", async ()
  }
 });

+it("retains unrelated withheld processes through cleanup, capture, and JSON", async () => {
+  const host: ProcessCaptureCleanupHost = {
+    platform: "darwin",
+    cleanupProcessGroup: async () => ({
+      cleaned: true,
+      signaled: true,
+      unverified: [
+        { pid: 900, diagnostic: "platform_binary_environment_withheld" },
+      ],
+    }),
+    verifyTokenOwnedProcesses: async () => ({
+      cleaned: true,
+      signaled: false,
+      unverified: [{ pid: 901, diagnostic: "foreign uid: EINVAL" }],
+    }),
+    removeTemporaryRoot: async () => undefined,
+  };
+  const report = await releaseProcessResources({
+    timers: new Set(),
+    terminal: { pid: 321 },
+    renderer: undefined,
+    runId: "fixture-run",
+    temporaryRoot: "/fixture/root",
+    host,
+  });
+  const unverified = [
+    { pid: 900, reason: "platform_binary_environment_withheld" },
+    { pid: 901, reason: "foreign uid: EINVAL" },
+  ];
+  expect(report.owned_process_group).toEqual({
+    state: "cleaned",
+    reason: null,
+    unverified_processes: unverified,
+  });
+  const original = emptyProcessCapture();
+  const { cleanup: previousCleanup, ...pending } = original;
+  for (const input of [pending, original]) {
+    const resolved = resolveProcessResult(input, undefined, report);
+    const serialized: unknown = JSON.parse(JSON.stringify(resolved));
+    const capture = parseProcessCapture(serialized);
+    expect(capture.cleanup).toEqual({
+      ...previousCleanup,
+      unverified_processes: unverified,
+    });
+    expect(capture.residual_unknowns).toEqual([
+      ...original.residual_unknowns,
+      {
+        scope: "process",
+        reason: expect.stringContaining("900 could not be verified"),
+      },
+      {
+        scope: "process",
+        reason: expect.stringContaining("901 could not be verified"),
+      },
+    ]);
+  }
+});
+
 it("retains the last ownership failure when the verification grace expires", async () => {
  vi.useFakeTimers();
  try {
@@ -246,6 +304,9 @@ it("retains observations and both causes when process cleanup is unverifiable",
      state: "unverified" as const,
      reason:
        "process ownership token could not be read for 1 live process(es): environment_unavailable=1",
+      unverified_processes: [
+        { pid: 900, reason: "platform_binary_environment_withheld" },
+      ],
    },
    terminal_renderer: { state: "cleaned" as const, reason: null },
    temporary_root: { state: "cleaned" as const, reason: null },
@@ -24,7 +24,7 @@ cliTest(
      join(root, "files", "modules", "main.js"),
      artifacts.source,
    );
-    const manifestPath = join(root, "manifest.json");
+    const manifestPath = join(root, "manifest.json").replaceAll("\\", "/");
    await writeFile(manifestPath, JSON.stringify(manifest));
    const environment = {
      REA_LOG_LEVEL: "silent",
@@ -1,4 +1,10 @@
-import { expect } from "vitest";
+import { expect, onTestFinished } from "vitest";
+import { Client } from "@modelcontextprotocol/client";
+import {
+  StdioClientTransport,
+  getDefaultEnvironment,
+} from "@modelcontextprotocol/client/stdio";
+import { fileURLToPath } from "node:url";
 import { mkdir, writeFile } from "node:fs/promises";
 import { join } from "node:path";
 import { webSourceLocationFixture } from "../fixtures/webSourceLocation.js";
@@ -12,7 +18,7 @@ cliTest(
    const fixture = webSourceLocationFixture();
    await mkdir(join(root, "files", "modules"), { recursive: true });
    await writeFile(join(root, "files", "modules", "main.js"), fixture.source);
-    const manifest = join(root, "manifest.json");
+    const manifest = join(root, "manifest.json").replaceAll("\\", "/");
    const map = join(root, "app.js.map");
    await writeFile(manifest, JSON.stringify(fixture.manifest));
    await writeFile(map, fixture.sourceMap.text);
@@ -44,6 +50,40 @@ cliTest(
        runtime: { id: "node-v8" },
      },
    });
+    const transport = new StdioClientTransport({
+      command: process.execPath,
+      args: [
+        fileURLToPath(new URL("../../scripts/rea.mjs", import.meta.url)),
+        "mcp",
+      ],
+      env: { ...getDefaultEnvironment(), REA_LOG_LEVEL: "silent" },
+      stderr: "pipe",
+    });
+    const client = new Client({
+      name: "source-location-cli-parity",
+      version: "1",
+    });
+    onTestFinished(async () => {
+      try {
+        await client.close();
+      } finally {
+        await transport.close();
+      }
+    });
+    await client.connect(transport);
+    const mcpResponse = await client.callTool({
+      name: "trace_web_source_location",
+      arguments: {
+        manifest_path: manifest,
+        script_index: 0,
+        source_map: { path: map, url: fixture.sourceMap.url },
+        generated_position: { line: 1, column: 0 },
+      },
+    });
+    expect(mcpResponse.isError, JSON.stringify(mcpResponse)).not.toBe(true);
+    expect(mcpResponse.structuredContent).toMatchObject({
+      evidence: response.json,
+    });
    const invalid = await cli.run({
      arguments: [
        "trace-web-source-location",
@@ -95,7 +95,7 @@ describe("canonical product catalog", () => {
      );
  });

-  it("matches every source-derived checked-in product fact", async () => {
+  it("matches every source-derived build-generated product fact", async () => {
    const catalog = await createProductCatalog(root);
    expect(catalog.tools.total).toBe(TOOL_CONTRACTS.length);
    expect(
@@ -195,14 +195,19 @@ describe("canonical product catalog", () => {
      "project_managed_application_graph",
      "verify_managed_native_boundaries",
    ]);
+    // Runtime schema commitments must not fan out into checked-in documentation.
+    // Provider commitments cover the facts actually present in this projection.
+    expect(Object.keys(catalog.runtime_catalog.digests)).toEqual([
+      "providers_sha256",
+    ]);
    expect(catalog.runtime_catalog.digests.providers_sha256).toBe(
      providerCatalogDigest(catalog.providers),
    );
    expect(
-      JSON.parse(await readFile("docs/product-catalog.json", "utf8")),
+      JSON.parse(await readFile("docs/public/product-catalog.json", "utf8")),
    ).toEqual(catalog);
    expect(await serializeProductCatalog(catalog)).toBe(
-      await readFile("docs/product-catalog.json", "utf8"),
+      await readFile("docs/public/product-catalog.json", "utf8"),
    );
    await expect(
      assertDocumentationFacts(root, catalog),
@@ -164,7 +164,7 @@ const createBuildCacheFixture = async (): Promise<string> => {
    "scripts/clean-build-output.mjs",
    "scripts/generate-package-metadata.mjs",
    "scripts/lib/generated-file.mjs",
-    "skills/reverse-engineer-anything/SKILL.md",
+    "skill-src/reverse-engineer-anything/SKILL.md",
    "src/generatedPackageMetadata.ts",
  ];
  await Promise.all(
@@ -10,6 +10,7 @@ import {
  writeEvidenceBundle,
 } from "../../../src/application/EvidenceBundleFiles.js";
 import { compareEvidenceBundlesCommand } from "../../../src/application/EvidenceBundleCommands.js";
+import { projectAnalysisError } from "../../../src/domain/analysisErrorProjection.js";
 import { createEvidence } from "../../../src/domain/evidence.js";
 import {
  createEvidenceBundle,
@@ -116,6 +117,32 @@ describe("evidence bundle filesystem adapter", () => {
    });
  });

+  it("reports a missing file or output directory with the selected path", async () => {
+    const directory = await createTestTempDirectory("rea-evidence-");
+    const absent = join(directory, "absent.json");
+    const read = await readEvidenceBundle(absent);
+    expect(read).toMatchObject({
+      ok: false,
+      error: { _tag: "EvidenceFileError", reason: "missing", path: absent },
+    });
+    if (read.ok) throw new Error("Expected a missing-file failure");
+    expect(projectAnalysisError(read.error)).toMatchObject({
+      message: expect.stringContaining("does not exist at the selected path"),
+      details: { operation: "read", reason: "missing", path: absent },
+    });
+
+    const orphan = join(directory, "absent", "bundle.json");
+    const written = await writeEvidenceBundle(bundle(), orphan, false);
+    expect(written).toMatchObject({
+      ok: false,
+      error: { _tag: "EvidenceFileError", reason: "missing", path: orphan },
+    });
+    if (written.ok) throw new Error("Expected a missing-directory failure");
+    expect(projectAnalysisError(written.error).message).toContain(
+      "output directory does not exist",
+    );
+  });
+
  it("rejects malformed and tampered input", async () => {
    const directory = await createTestTempDirectory("rea-evidence-");
    const malformed = join(directory, "malformed.json");
@@ -136,7 +163,55 @@ describe("evidence bundle filesystem adapter", () => {
    );
    expect(await readEvidenceBundle(tamperedPath)).toMatchObject({
      ok: false,
-      error: { _tag: "EvidenceIntegrityError" },
+      error: {
+        _tag: "EvidenceIntegrityError",
+        userMessage: expect.stringContaining(
+          "Evidence semantic identifier does not match its record",
+        ),
+      },
+    });
+  });
+
+  it("names the failed bundle constraint for a single record or schema mismatch", async () => {
+    const directory = await createTestTempDirectory("rea-evidence-");
+    const record = bundle().records[0];
+    const single = join(directory, "record.json");
+    await writeFile(single, JSON.stringify(record));
+    expect(await readEvidenceBundle(single)).toMatchObject({
+      ok: false,
+      error: {
+        _tag: "EvidenceIntegrityError",
+        userMessage: expect.stringContaining(
+          `this JSON is one Evidence record (${String(record?.evidence_id)})`,
+        ),
+      },
+    });
+
+    const partial = join(directory, "partial.json");
+    await writeFile(partial, JSON.stringify({ evidence_id: "typo" }));
+    const rejected = await readEvidenceBundle(partial);
+    expect(rejected).toMatchObject({
+      ok: false,
+      error: {
+        userMessage: expect.stringContaining(
+          "does not match the bundle schema",
+        ),
+      },
+    });
+    expect(rejected).not.toMatchObject({
+      error: { userMessage: expect.stringContaining("one Evidence record") },
+    });
+
+    const mismatched = join(directory, "mismatched.json");
+    await writeFile(mismatched, JSON.stringify({ ...bundle(), records: {} }));
+    expect(await readEvidenceBundle(mismatched)).toMatchObject({
+      ok: false,
+      error: {
+        _tag: "EvidenceIntegrityError",
+        userMessage: expect.stringContaining(
+          "does not match the bundle schema at records:",
+        ),
+      },
    });
  });
 });
@@ -0,0 +1,125 @@
+import { execFile } from "node:child_process";
+import { copyFile, mkdir, readFile, rm, writeFile } from "node:fs/promises";
+import { dirname, join } from "node:path";
+import { fileURLToPath } from "node:url";
+import { promisify } from "node:util";
+import { expect, it } from "vitest";
+
+import { createTestTempDirectory } from "../../fixtures/temporaryDirectory.js";
+
+const exec = promisify(execFile);
+const repositoryRoot = fileURLToPath(new URL("../../..", import.meta.url));
+const authored =
+  '---\nname: reverse-engineer-anything\nmetadata:\n  version: "33"\n---\n\n# Instructions\n\nInspect the caller-selected artifact.\n';
+
+async function fixture(eol = "\n") {
+  const root = await createTestTempDirectory("rea-generated-skill-");
+  for (const path of [
+    "scripts/generate-skill-metadata.mjs",
+    "scripts/lib/generated-file.mjs",
+  ]) {
+    await mkdir(dirname(join(root, path)), { recursive: true });
+    await copyFile(join(repositoryRoot, path), join(root, path));
+  }
+  const sourceRoot = join(root, "skill-src/reverse-engineer-anything");
+  const outputRoot = join(root, "skills/reverse-engineer-anything");
+  await mkdir(join(sourceRoot, "references"), { recursive: true });
+  await mkdir(join(root, "dist"));
+  await writeFile(join(root, "package.json"), '{"type":"module"}\n');
+  await writeFile(join(sourceRoot, "SKILL.md"), authored.replaceAll("\n", eol));
+  await writeFile(
+    join(sourceRoot, "references/guide.md"),
+    `# Guide${eol}Preserve evidence.${eol}`,
+  );
+  const identity = async (count: number, digest: string) =>
+    writeFile(
+      join(root, "dist/catalogIdentity.js"),
+      `export const CATALOG_IDENTITY = ${JSON.stringify({ counts: { mcp_tools: count }, digests: { combined_sha256: digest } })};\n`,
+    );
+  await identity(139, "a".repeat(64));
+  const generate = (...args: string[]) =>
+    exec(
+      process.execPath,
+      [join(root, "scripts/generate-skill-metadata.mjs"), ...args],
+      { cwd: root },
+    );
+  return { sourceRoot, outputRoot, identity, generate };
+}
+
+it.each(["\n", "\r\n"])(
+  "generates revision-specific metadata without rewriting authored instructions (%j)",
+  async (eol) => {
+    const f = await fixture(eol);
+    await f.generate();
+    const first = await readFile(join(f.outputRoot, "SKILL.md"), "utf8");
+    expect(first).not.toContain("catalog_digest:");
+    expect(first).toContain("tool_count: 139");
+    expect(
+      first.replace(/^ {2}(?:tool_count|catalog_digest):[^\n]*\n/gmu, ""),
+    ).toBe(authored);
+    expect(
+      await readFile(join(f.outputRoot, "references/guide.md"), "utf8"),
+    ).toBe("# Guide\nPreserve evidence.\n");
+    await f.identity(139, "b".repeat(64));
+    await f.generate();
+    expect(await readFile(join(f.outputRoot, "SKILL.md"), "utf8")).toBe(first);
+    await f.identity(140, "b".repeat(64));
+    await expect(f.generate("--check")).rejects.toMatchObject({
+      stderr: expect.stringContaining("missing or stale"),
+    });
+    await f.generate();
+    expect(await readFile(join(f.outputRoot, "SKILL.md"), "utf8")).toContain(
+      "tool_count: 140",
+    );
+    expect(await readFile(join(f.sourceRoot, "SKILL.md"), "utf8")).toBe(
+      authored.replaceAll("\n", eol),
+    );
+    expect(
+      await readFile(join(f.sourceRoot, "references/guide.md"), "utf8"),
+    ).toBe(`# Guide${eol}Preserve evidence.${eol}`);
+    await expect(f.generate("--check")).resolves.toMatchObject({ stderr: "" });
+  },
+);
+
+it("rejects missing, stale, and extra packaged references and removes deleted source files on rebuild", async () => {
+  const f = await fixture();
+  await f.generate();
+  const guide = join(f.outputRoot, "references/guide.md");
+  await rm(guide);
+  await expect(f.generate("--check")).rejects.toMatchObject({
+    stderr: expect.stringContaining("guide.md is missing or stale"),
+  });
+  await f.generate();
+  await writeFile(guide, "modified reference\n");
+  await expect(f.generate("--check")).rejects.toMatchObject({
+    stderr: expect.stringContaining("guide.md is missing or stale"),
+  });
+  await f.generate();
+  await writeFile(
+    join(f.outputRoot, "references/removed.md"),
+    "obsolete instructions\n",
+  );
+  await expect(f.generate("--check")).rejects.toMatchObject({
+    stderr: expect.stringContaining("file inventory drifted"),
+  });
+  await rm(join(f.sourceRoot, "references/guide.md"));
+  await f.generate();
+  await expect(readFile(guide)).rejects.toMatchObject({ code: "ENOENT" });
+  await expect(
+    readFile(join(f.outputRoot, "references/removed.md")),
+  ).rejects.toMatchObject({ code: "ENOENT" });
+  await f.generate("--check");
+});
+
+it("rejects catalog-dependent metadata in the authored source", async () => {
+  const f = await fixture();
+  await writeFile(
+    join(f.sourceRoot, "SKILL.md"),
+    authored.replace('  version: "33"', '  version: "33"\n  tool_count: 139'),
+  );
+  await expect(f.generate()).rejects.toMatchObject({
+    stderr: expect.stringContaining(
+      "Catalog metadata belongs in the generated skill",
+    ),
+  });
+});
@@ -0,0 +1,99 @@
+import { mkdir, writeFile } from "node:fs/promises";
+import { join } from "node:path";
+
+import { build } from "plist";
+import { expect, it } from "vitest";
+
+import { ArtifactReaderFailure } from "../../../src/artifacts/ArtifactReader.js";
+import { inspectBundleKeyedArchive } from "../../../src/artifacts/apple/KeyedArchiveReader.js";
+import { AnalysisInputError } from "../../../src/domain/analysisErrorCore.js";
+import { createTestTempDirectory } from "../../fixtures/temporaryDirectory.js";
+
+const archive = build({
+  $archiver: "NSKeyedArchiver",
+  $version: 100000,
+  $objects: ["$null", "value"],
+  $top: { root: { CF$UID: 1 }, other: { CF$UID: 1 } },
+});
+
+const bundle = async () => {
+  const root = await createTestTempDirectory("rea-keyed-selection-");
+  await mkdir(join(root, "Contents", "Resources"), { recursive: true });
+  await writeFile(
+    join(root, "Contents", "Resources", "Model.plist"),
+    Buffer.from(archive),
+  );
+  return root;
+};
+
+const inspect = (bundlePath: string, parameters: Record<string, unknown>) =>
+  inspectBundleKeyedArchive({
+    bundlePath,
+    targetSha256: "a".repeat(64),
+    parameters,
+  });
+
+it.each([
+  [".", "invalid_format", "relative to the active app bundle"],
+  ["Contents/../Model.plist", "invalid_format", "canonical relative"],
+  ["Contents//Model.plist", "invalid_format", "canonical relative"],
+  ["Contents/Resources", "invalid_value", "selects a directory"],
+  ["Contents/Resources/Missing.plist", "invalid_value", "No regular file"],
+] as const)(
+  "reports caller-selected archive path %j as invalid input",
+  async (path, reason, message) => {
+    const root = await bundle();
+    const rejected = await inspect(root, { path }).catch(
+      (cause: unknown) => cause,
+    );
+    expect(rejected).toBeInstanceOf(AnalysisInputError);
+    expect(rejected).toMatchObject({
+      issues: [
+        {
+          path: ["path"],
+          reason,
+          message: expect.stringContaining(message),
+        },
+      ],
+    });
+  },
+);
+
+it("reports an absent named root with the archive's available roots", async () => {
+  const root = await bundle();
+  await expect(
+    inspect(root, { path: "Contents/Resources/Model.plist", root: "missing" }),
+  ).rejects.toMatchObject({
+    issues: [
+      {
+        path: ["root"],
+        reason: "invalid_value",
+        message: expect.stringContaining("missing"),
+        expected: ["root", "other"],
+      },
+    ],
+  });
+});
+
+it.each([
+  ["plain plist", Buffer.from(build({ plain: true })), "NSKeyedArchiver"],
+  [
+    "compiled NIBArchive",
+    Buffer.concat([Buffer.from("NIBArchive"), Buffer.alloc(40)]),
+    "decode_interface_builder",
+  ],
+])(
+  "keeps the decoder reason for a selected %s",
+  async (_label, bytes, detail) => {
+    const root = await bundle();
+    await writeFile(join(root, "Contents", "Resources", "Other.nib"), bytes);
+    const rejected = await inspect(root, {
+      path: "Contents/Resources/Other.nib",
+    }).catch((cause: unknown) => cause);
+    expect(rejected).toBeInstanceOf(ArtifactReaderFailure);
+    expect(rejected).toMatchObject({
+      reason: "format",
+      message: expect.stringContaining(detail),
+    });
+  },
+);
@@ -50,7 +50,6 @@ async function metadata(directory: string, version: string, notes: string) {
      version,
      packages: [{ identifier: "rea-agents", version }],
    },
-    "docs/product-catalog.json": { package: { version } },
    "release-please-config.json": {
      "changelog-sections": [
        { type: "feat", hidden: false },
@@ -371,7 +370,6 @@ it("validates candidate options before inspecting the working directory", async
 it.each([
  "package-lock.json",
  "server.json",
-  "docs/product-catalog.json",
  "src/generatedPackageMetadata.ts",
 ])("rejects inconsistent version metadata in %s", async (path) => {
  const f = await fixture();
@@ -103,11 +103,11 @@ it("requires explicit release preparation or publication instead of main pushes"
    "skip-github-release": "${{ inputs.phase == 'prepare' }}",
    "skip-github-pull-request": "${{ inputs.phase == 'publish' }}",
  });
-  const catalogCommit = workflow.jobs["release-please"].steps.find(
-    (step) => step.name === "Commit canonical release catalog",
+  const catalogValidation = workflow.jobs["release-please"].steps.find(
+    (step) => step.name === "Validate generated release documentation",
  );
-  expect(catalogCommit?.env?.GH_TOKEN).toBe(
-    "${{ secrets.RELEASE_PLEASE_TOKEN || secrets.GITHUB_TOKEN }}",
+  expect(catalogValidation?.run).toBe(
+    "npm run docs:check && git diff --exit-code",
  );
 });

@@ -203,7 +203,7 @@ it("binds npm and MCP publication to the same immutable release SHA", async () =
    "Set up Node.js for generated documentation",
    "Install dependencies",
    "Regenerate release documentation",
-    "Commit canonical release catalog",
+    "Validate generated release documentation",
  ];
  for (const name of preparation) {
    expect(