test(hopper): cover verified Linux rejection

docs/investigation-workspaces.md

@@ -31,6 +31,11 @@ Use `--expected-revision N` when an external coordinator needs an explicit
 compare-and-swap guard. Traversal, byte, page, and comparison limits are also
 available as CLI options.
 
+After a completed run returns its stable run ID, `--replay-run-id RUN_ID`
+selects that exact result without reading or rescanning either version input.
+The workspace still requires read authority. REA rejects a selector that is
+missing, incomplete, or inconsistent with the requested paths and controls.
+
 ## MCP
 
 `find_changed_behavior` retains its existing aggregation mode. Its additive
@@ -75,6 +80,12 @@ report checkpoints. A process interrupted after a checkpoint can resume from
 the last complete stage. A completed run is reused when both graph commitments
 and every bounded option are identical.
 
+By default, REA rescans the version inputs so changed content creates a new
+run. For an explicit cache-only replay, add the returned `run_id` as
+`investigation_run.replay_run_id`. REA first validates the workspace revision,
+the complete run, its inventory paths and controls, and its linked Evidence;
+only then may it return without requesting input-read authority.
+
 The run ID is a SHA-256 commitment to both root and graph digests plus the
 normalized options. Local paths and timestamps do not affect that identity.
 Changing either artifact or a budget creates a new run in the same workspace;

scripts/scan-todos.mjs

@@ -6,21 +6,15 @@ import { relative, resolve } from "node:path";
 
 const root = resolve(import.meta.dirname, "..");
 
-// Collect all TS, MJS, and Python source files, excluding generated and third-party dirs.
-const sourceFiles = [
-  ...globSync("src/**/*.ts", {
+// Native globSync is available throughout the Node versions in package.engines.
+// Its exclusion option is `exclude`; `ignore` and `nodir` belong to npm glob.
+const sourceFiles = globSync(
+  ["src/**/*.ts", "tests/**/*.ts", "scripts/**/*.mjs", "bridge/**/*.py"],
+  {
     cwd: root,
-    nodir: true,
-    ignore: ["dist/**", "node_modules/**"],
-  }),
-  ...globSync("tests/**/*.ts", {
-    cwd: root,
-    nodir: true,
-    ignore: ["node_modules/**"],
-  }),
-  ...globSync("scripts/**/*.mjs", { cwd: root, nodir: true }),
-  ...globSync("bridge/**/*.py", { cwd: root, nodir: true }),
-];
+    exclude: (path) => path.split(/[\\/]/u).includes("node_modules"),
+  },
+);
 
 const patterns = [
   { regex: /TODO(?::\s*(.*))?$/gm, label: "TODO" },

scripts/verify-package.mjs

@@ -170,72 +170,88 @@ try {
     throw new Error("packaged artifact inventory CLI failed");
   // prettier-ignore
   await verifyPackagedInvestigation({ cli, workspace, evidenceRoot, artifactArchive, environment });
-  const overview = json(
-    await run(cli, ["analyze", process.execPath, "--json"], environment),
-  );
-  if (
-    overview.operation !== "binary_overview" ||
-    overview.normalized_result?.procedure_count < 1
-  )
-    throw new Error(
-      `packaged Hopper-backed analyze CLI failed: ${JSON.stringify(overview)}`,
+  if (process.platform === "linux") {
+    const unsupportedExecution = await runWithStatus(
+      cli,
+      ["analyze", process.execPath, "--json"],
+      environment,
     );
-  const inspected = json(
-    await run(
-      cli,
-      [
-        "inspect",
-        process.execPath,
-        "--detail",
-        "detailed",
-        "--limit",
-        "1",
-        "--json",
-      ],
-      environment,
-    ),
-  );
-  if (
-    inspected.operation !== "binary_overview" ||
-    inspected.normalized_result?.detail !== "detailed"
-  )
-    throw new Error("packaged inspect CLI failed");
-  const functionResult = json(
-    await run(
-      cli,
-      ["function", process.execPath, "0x1000", "--json"],
-      environment,
-    ),
-  );
-  if (
-    functionResult.operation !== "analyze_function" ||
-    functionResult.provider?.id !== "hopper" ||
-    functionResult.normalized_result?.procedure?.address !== "0x1000"
-  )
-    throw new Error(
-      `packaged function CLI failed: ${JSON.stringify(functionResult)}`,
+    const unsupported = json(unsupportedExecution.stdout);
+    if (
+      unsupportedExecution.status !== 1 ||
+      unsupported.details?.failure_code !== "unsupported_hopper_build"
+    )
+      throw new Error(
+        `packaged Linux Hopper verification did not fail closed: ${JSON.stringify(unsupported)}`,
+      );
+  } else {
+    const overview = json(
+      await run(cli, ["analyze", process.execPath, "--json"], environment),
     );
-  const xrefs = json(
-    await run(
-      cli,
-      ["xrefs", process.execPath, "0x1000", "--json"],
-      environment,
-    ),
-  );
-  if (
-    xrefs.operation !== "xrefs" ||
-    JSON.stringify(xrefs.normalized_result) !== JSON.stringify(["0x1000"])
-  )
-    throw new Error(`packaged xrefs CLI failed: ${JSON.stringify(xrefs)}`);
-  const trace = json(
-    await run(
-      cli,
-      ["trace", process.execPath, "fixture", "--json"],
-      environment,
-    ),
-  );
-  if (trace.operation !== "trace_feature")
-    throw new Error(`packaged trace CLI failed: ${JSON.stringify(trace)}`);
+    if (
+      overview.operation !== "binary_overview" ||
+      overview.normalized_result?.procedure_count < 1
+    )
+      throw new Error(
+        `packaged Hopper-backed analyze CLI failed: ${JSON.stringify(overview)}`,
+      );
+    const inspected = json(
+      await run(
+        cli,
+        [
+          "inspect",
+          process.execPath,
+          "--detail",
+          "detailed",
+          "--limit",
+          "1",
+          "--json",
+        ],
+        environment,
+      ),
+    );
+    if (
+      inspected.operation !== "binary_overview" ||
+      inspected.normalized_result?.detail !== "detailed"
+    )
+      throw new Error("packaged inspect CLI failed");
+    const functionResult = json(
+      await run(
+        cli,
+        ["function", process.execPath, "0x1000", "--json"],
+        environment,
+      ),
+    );
+    if (
+      functionResult.operation !== "analyze_function" ||
+      functionResult.provider?.id !== "hopper" ||
+      functionResult.normalized_result?.procedure?.address !== "0x1000"
+    )
+      throw new Error(
+        `packaged function CLI failed: ${JSON.stringify(functionResult)}`,
+      );
+    const xrefs = json(
+      await run(
+        cli,
+        ["xrefs", process.execPath, "0x1000", "--json"],
+        environment,
+      ),
+    );
+    if (
+      xrefs.operation !== "xrefs" ||
+      JSON.stringify(xrefs.normalized_result) !== JSON.stringify(["0x1000"])
+    )
+      throw new Error(`packaged xrefs CLI failed: ${JSON.stringify(xrefs)}`);
+    const trace = json(
+      await run(
+        cli,
+        ["trace", process.execPath, "fixture", "--json"],
+        environment,
+      ),
+    );
+    if (trace.operation !== "trace_feature")
+      throw new Error(`packaged trace CLI failed: ${JSON.stringify(trace)}`);
+  }
   const capabilities = json(
     await run(cli, ["capabilities", "--json"], environment),
   );
@@ -247,20 +263,22 @@ try {
     providers.providers.some(({ id }) => typeof id !== "string")
   )
     throw new Error("packaged providers CLI failed");
-  const searchResult = json(
-    await run(
-      cli,
-      ["search", process.execPath, "fixture", "--json"],
-      environment,
-    ),
-  );
-  if (
-    searchResult.operation !== "search_strings" ||
-    searchResult.normalized_result?.items?.length !== 1
-  )
-    throw new Error(
-      `packaged search CLI failed: ${JSON.stringify(searchResult)}`,
+  if (process.platform !== "linux") {
+    const searchResult = json(
+      await run(
+        cli,
+        ["search", process.execPath, "fixture", "--json"],
+        environment,
+      ),
     );
+    if (
+      searchResult.operation !== "search_strings" ||
+      searchResult.normalized_result?.items?.length !== 1
+    )
+      throw new Error(
+        `packaged search CLI failed: ${JSON.stringify(searchResult)}`,
+      );
+  }
   const referenceImport = json(
     await run(
       cli,
@@ -478,30 +496,41 @@ try {
     );
     if (opened.isError === true)
       throw new Error("packaged MCP could not open a binary");
-    await prompts.verifyPromptCompletion(client, mcpOptions, true);
+    await prompts.verifyPromptCompletion(
+      client,
+      mcpOptions,
+      process.platform !== "linux",
+    );
     const current = await client.callTool(
       { name: "current_document", arguments: {} },
       mcpOptions,
     );
-    if (
-      current.isError === true ||
-      json(prompts.mcpText(current)).normalized_result !== "fixture"
-    )
-      throw new Error("packaged MCP bridge call failed");
-    const batch = await client.callTool(
-      { name: "batch_decompile", arguments: { addresses: ["0x1000"] } },
-      mcpOptions,
-    );
-    const batchResult = json(prompts.mcpText(batch)).normalized_result;
-    if (
-      batch.isError === true ||
-      batchResult?.total !== 1 ||
-      batchResult?.succeeded !== 1 ||
-      batchResult?.failed !== 0 ||
-      batchResult?.items?.[0]?.status !== "ok" ||
-      batchResult?.items?.[0]?.pseudocode !== "return 0;"
-    )
-      throw new Error("packaged MCP structured batch result failed");
+    if (process.platform === "linux") {
+      if (
+        current.isError !== true ||
+        !prompts
+          .mcpText(current)
+          .includes("not supported for unattended Linux analysis")
+      )
+        throw new Error("packaged Linux MCP did not reject an unpinned Hopper");
+    } else {
+      if (json(prompts.mcpText(current)).normalized_result !== "fixture")
+        throw new Error("packaged MCP bridge call failed");
+      const batch = await client.callTool(
+        { name: "batch_decompile", arguments: { addresses: ["0x1000"] } },
+        mcpOptions,
+      );
+      const batchResult = json(prompts.mcpText(batch)).normalized_result;
+      if (
+        batch.isError === true ||
+        batchResult?.total !== 1 ||
+        batchResult?.succeeded !== 1 ||
+        batchResult?.failed !== 0 ||
+        batchResult?.items?.[0]?.status !== "ok" ||
+        batchResult?.items?.[0]?.pseudocode !== "return 0;"
+      )
+        throw new Error("packaged MCP structured batch result failed");
+    }
     const closed = await client.callTool(
       { name: "close_binary", arguments: {} },
       mcpOptions,

src/application/CrossVersionInvestigation.ts

@@ -45,6 +45,7 @@ import {
   ARTIFACT_COMPARISON_PROVIDER,
   CHANGED_BEHAVIOR_PROVIDER,
 } from "./InvestigationProviders.js";
+import { selectCompletedInvestigationReplay } from "./CrossVersionInvestigationReplay.js";
 
 export interface CrossVersionInvestigationOutcome {
   readonly evidence: Evidence;
@@ -59,6 +60,7 @@ export interface CrossVersionInvestigationExecution {
   readonly signal?: AbortSignal;
   readonly progress?: ProgressReporter;
   readonly integrityContinueEnabled?: boolean;
+  readonly authorizeInputRead?: () => Promise<Result<null, AnalysisError>>;
   readonly authorizeWorkspaceWrite?: () => Promise<Result<null, AnalysisError>>;
 }
 
@@ -84,6 +86,23 @@ export const runCrossVersionInvestigation = async (
   if (!preflight.ok) return preflight;
   if (isCancelled(execution.signal))
     return err(new AnalysisCancelledError("find_changed_behavior"));
+  if (parsed.data.replay_run_id !== undefined) {
+    const replay = selectCompletedInvestigationReplay(
+      initial.value,
+      parsed.data,
+    );
+    if (!replay.ok) return replay;
+    return completeOutcome(
+      replay.value.workspace,
+      replay.value.run,
+      true,
+      execution.session,
+    );
+  }
+  if (execution.authorizeInputRead !== undefined) {
+    const authorized = await execution.authorizeInputRead();
+    if (!authorized.ok) return authorized;
+  }
   await execution.progress?.report({
     phase: "scan_versions",
     completed: 0,

src/application/CrossVersionInvestigationReplay.ts

@@ -0,0 +1,372 @@
+import {
+  changedBehaviorResultSchema,
+  type ChangedBehaviorResult,
+} from "../domain/changedBehavior.js";
+import { artifactInventoryResultSchema } from "../domain/artifactGraph.js";
+import { parseArtifactInventoryEvidence } from "../domain/artifactInventoryEvidence.js";
+import type { Evidence } from "../domain/evidence.js";
+import {
+  EvidenceIntegrityError,
+  InvestigationWorkspaceError,
+} from "../domain/errors.js";
+import type {
+  CrossVersionInvestigationInput,
+  InvestigationRun,
+  InvestigationWorkspace,
+} from "../domain/investigationWorkspace.js";
+import { err, ok, type Result } from "../domain/result.js";
+import {
+  ARTIFACT_COMPARISON_PROVIDER,
+  ARTIFACT_GRAPH_PROVIDER,
+  CHANGED_BEHAVIOR_PROVIDER,
+} from "./InvestigationProviders.js";
+
+/** Validated workspace state returned by an explicit replay selector. */
+export interface CompletedInvestigationReplay {
+  readonly workspace: InvestigationWorkspace;
+  readonly run: InvestigationRun;
+}
+
+/** Select and verify one caller-identified complete run without input access. */
+export const selectCompletedInvestigationReplay = (
+  workspace: InvestigationWorkspace | null,
+  input: CrossVersionInvestigationInput,
+): Result<
+  CompletedInvestigationReplay,
+  InvestigationWorkspaceError | EvidenceIntegrityError
+> => {
+  const run = workspace?.runs.find(
+    ({ run_id: runId }) => runId === input.replay_run_id,
+  );
+  if (workspace === null || run === undefined || run.status !== "complete")
+    return err(new InvestigationWorkspaceError("read", "revision-conflict"));
+  if (!replayRequestMatches(workspace, run, input))
+    return err(new InvestigationWorkspaceError("read", "revision-conflict"));
+  const evidence = validateCompletedReplayEvidence(workspace, run);
+  return evidence.ok ? ok({ workspace, run }) : evidence;
+};
+
+const replayRequestMatches = (
+  workspace: InvestigationWorkspace,
+  run: InvestigationRun,
+  input: CrossVersionInvestigationInput,
+): boolean =>
+  JSON.stringify(run.options) === JSON.stringify(input.options) &&
+  run.integrity_policy === input.integrity_policy &&
+  run.integrity_continue_approved === input.integrity_continue_approved &&
+  run.max_integrity_mismatches === input.max_integrity_mismatches &&
+  inventoryEvidenceMatches(workspace, run.left_inventory_evidence_ids, {
+    path: input.left_path,
+    target: run.left,
+    input,
+  }) &&
+  inventoryEvidenceMatches(workspace, run.right_inventory_evidence_ids, {
+    path: input.right_path,
+    target: run.right,
+    input,
+  });
+
+interface InventoryReplayExpectation {
+  readonly path: string;
+  readonly target: InvestigationRun["left"];
+  readonly input: CrossVersionInvestigationInput;
+}
+
+const inventoryEvidenceMatches = (
+  workspace: InvestigationWorkspace,
+  evidenceIds: readonly string[],
+  expectation: InventoryReplayExpectation,
+): boolean => {
+  const byId = new Map(
+    workspace.bundle.records.map((record) => [record.evidence_id, record]),
+  );
+  const evidence = evidenceIds.flatMap((evidenceId) => {
+    const record = byId.get(evidenceId);
+    return record === undefined ? [] : [record];
+  });
+  if (
+    evidence.length !== evidenceIds.length ||
+    !evidence.every((record, index) =>
+      inventoryPageMatches(record, index, expectation),
+    )
+  )
+    return false;
+  try {
+    const inventory = parseArtifactInventoryEvidence(evidence).inventory;
+    return (
+      inventory.complete &&
+      evidence.length ===
+        expectedInventoryPageCount(
+          inventory.manifest.node_count,
+          inventory.manifest.occurrence_count,
+          inventory.manifest.edge_count,
+          expectation.input.options.page_size,
+        ) &&
+      inventory.manifest.root_sha256 === expectation.target.root_sha256 &&
+      inventory.manifest.graph_sha256 === expectation.target.graph_sha256 &&
+      inventory.manifest.manifest_id === expectation.target.manifest_id &&
+      inventory.manifest.root_format === expectation.target.format
+    );
+  } catch {
+    return false;
+  }
+};
+
+const inventoryPageMatches = (
+  evidence: Evidence,
+  index: number,
+  expectation: InventoryReplayExpectation,
+): boolean => {
+  const page = artifactInventoryResultSchema.safeParse(
+    evidence.normalized_result,
+  );
+  if (!page.success) return false;
+  const offset = index * expectation.input.options.page_size;
+  return (
+    inventoryEvidenceMetadataMatches(evidence, expectation) &&
+    inventoryParametersMatch(evidence.parameters, offset, expectation.input) &&
+    inventoryResultPageMatches(page.data, offset, expectation.input)
+  );
+};
+
+const inventoryEvidenceMetadataMatches = (
+  evidence: Evidence,
+  expectation: InventoryReplayExpectation,
+): boolean =>
+  evidence.operation === "inventory_artifact" &&
+  evidence.predicate_type === "rea.analysis/v2" &&
+  providerMatches(evidence.provider, ARTIFACT_GRAPH_PROVIDER) &&
+  evidence.subject?.local_path === expectation.path &&
+  evidence.subject.digest.sha256 === expectation.target.root_sha256 &&
+  evidence.subject.format === expectation.target.format &&
+  evidence.confidence === "observed" &&
+  evidence.authority === "shipped-artifact" &&
+  evidence.raw_result === null &&
+  evidence.environment === null &&
+  evidence.evidence_links.length === 0;
+
+const inventoryResultPageMatches = (
+  page: ReturnType<typeof artifactInventoryResultSchema.parse>,
+  offset: number,
+  input: CrossVersionInvestigationInput,
+): boolean =>
+  collectionPageMatches(
+    page.nodes,
+    offset,
+    input.options.page_size,
+    page.manifest.node_count,
+  ) &&
+  collectionPageMatches(
+    page.occurrences,
+    offset,
+    input.options.page_size,
+    page.manifest.occurrence_count,
+  ) &&
+  collectionPageMatches(
+    page.edges,
+    offset,
+    input.options.page_size,
+    page.manifest.edge_count,
+  ) &&
+  valuesMatch(page.limits, traversalLimits(input));
+
+const collectionPageMatches = (
+  page: {
+    readonly items: readonly unknown[];
+    readonly offset: number;
+    readonly limit: number;
+    readonly total: number;
+    readonly next_offset: number | null;
+  },
+  offset: number,
+  limit: number,
+  total: number,
+): boolean => {
+  const expectedItems = Math.max(0, Math.min(limit, total - offset));
+  const nextOffset = offset + limit < total ? offset + limit : null;
+  return (
+    page.offset === offset &&
+    page.limit === limit &&
+    page.total === total &&
+    page.items.length === expectedItems &&
+    page.next_offset === nextOffset
+  );
+};
+
+const expectedInventoryPageCount = (
+  nodeCount: number,
+  occurrenceCount: number,
+  edgeCount: number,
+  pageSize: number,
+): number =>
+  Math.max(
+    1,
+    Math.ceil(nodeCount / pageSize),
+    Math.ceil(occurrenceCount / pageSize),
+    Math.ceil(edgeCount / pageSize),
+  );
+
+const inventoryParametersMatch = (
+  parameters: Readonly<Record<string, unknown>>,
+  offset: number,
+  input: CrossVersionInvestigationInput,
+): boolean =>
+  Object.keys(parameters).length === 15 &&
+  parameters.node_offset === offset &&
+  parameters.node_limit === input.options.page_size &&
+  parameters.occurrence_offset === offset &&
+  parameters.occurrence_limit === input.options.page_size &&
+  parameters.edge_offset === offset &&
+  parameters.edge_limit === input.options.page_size &&
+  parameters.max_entries === input.options.max_entries &&
+  parameters.max_total_bytes === input.options.max_total_bytes &&
+  parameters.max_entry_bytes === input.options.max_entry_bytes &&
+  parameters.max_compression_ratio === input.options.max_compression_ratio &&
+  parameters.max_depth === input.options.max_depth &&
+  parameters.max_path_bytes === input.options.max_path_bytes &&
+  parameters.integrity_policy === input.integrity_policy &&
+  parameters.integrity_continue_approved ===
+    input.integrity_continue_approved &&
+  parameters.max_integrity_mismatches === input.max_integrity_mismatches;
+
+const traversalLimits = (input: CrossVersionInvestigationInput) => ({
+  max_entries: input.options.max_entries,
+  max_total_bytes: input.options.max_total_bytes,
+  max_entry_bytes: input.options.max_entry_bytes,
+  max_compression_ratio: input.options.max_compression_ratio,
+  max_depth: input.options.max_depth,
+  max_path_bytes: input.options.max_path_bytes,
+});
+
+const validateCompletedReplayEvidence = (
+  workspace: InvestigationWorkspace,
+  run: InvestigationRun,
+): Result<null, EvidenceIntegrityError> => {
+  const inventoryIds = [
+    ...run.left_inventory_evidence_ids,
+    ...run.right_inventory_evidence_ids,
+  ];
+  const comparison = workspace.bundle.records.find(
+    ({ evidence_id: evidenceId }) => evidenceId === run.comparison_evidence_id,
+  );
+  if (!comparisonEvidenceMatches(comparison, inventoryIds, run))
+    return inconsistentReplayEvidence();
+  const resultLinks = [
+    ...new Set([comparison.evidence_id, ...inventoryIds]),
+  ].sort((left, right) => left.localeCompare(right, "en"));
+  const result = workspace.bundle.records.find(
+    ({ evidence_id: evidenceId }) => evidenceId === run.result_evidence_id,
+  );
+  if (!resultEvidenceMatches(result, resultLinks, workspace, run))
+    return inconsistentReplayEvidence();
+  const parsedResult = changedBehaviorResultSchema.safeParse(
+    result.normalized_result,
+  );
+  if (
+    !parsedResult.success ||
+    !resultPayloadMatches(parsedResult.data, resultLinks, workspace, run)
+  )
+    return inconsistentReplayEvidence();
+  return ok(null);
+};
+
+const comparisonEvidenceMatches = (
+  comparison: Evidence | undefined,
+  inventoryIds: readonly string[],
+  run: InvestigationRun,
+): comparison is Evidence =>
+  comparison?.operation === "compare_artifacts" &&
+  comparison.predicate_type === "rea.artifact-comparison/v1" &&
+  providerMatches(comparison.provider, ARTIFACT_COMPARISON_PROVIDER) &&
+  comparison.subject === null &&
+  comparison.confidence === "derived" &&
+  comparison.authority === "analyst-inference" &&
+  valuesMatch(comparison.evidence_links, inventoryIds) &&
+  comparisonParametersMatch(comparison.parameters, run);
+
+const resultEvidenceMatches = (
+  result: Evidence | undefined,
+  resultLinks: readonly string[],
+  workspace: InvestigationWorkspace,
+  run: InvestigationRun,
+): result is Evidence =>
+  result?.operation === "find_changed_behavior" &&
+  result.predicate_type === "rea.changed-behavior/v1" &&
+  providerMatches(result.provider, CHANGED_BEHAVIOR_PROVIDER) &&
+  result.subject === null &&
+  result.confidence === "derived" &&
+  result.authority === "analyst-inference" &&
+  valuesMatch(result.evidence_links, resultLinks) &&
+  resultParametersMatch(result.parameters, workspace, run);
+
+const resultPayloadMatches = (
+  result: ChangedBehaviorResult,
+  resultLinks: readonly string[],
+  workspace: InvestigationWorkspace,
+  run: InvestigationRun,
+): boolean => {
+  const summary = result.investigation_run;
+  return (
+    summary?.workspace_id === workspace.workspace_id &&
+    summary.run_id === run.run_id &&
+    summary.left_manifest_id === run.left.manifest_id &&
+    summary.right_manifest_id === run.right.manifest_id &&
+    summary.inventory_evidence_count ===
+      run.left_inventory_evidence_ids.length +
+        run.right_inventory_evidence_ids.length &&
+    summary.comparison_evidence_id === run.comparison_evidence_id &&
+    valuesMatch(summary.limitations, run.limitations) &&
+    valuesMatch(result.evidence_links, resultLinks)
+  );
+};
+
+const inconsistentReplayEvidence = (): Result<never, EvidenceIntegrityError> =>
+  err(
+    new EvidenceIntegrityError(
+      "Completed investigation replay Evidence is inconsistent",
+    ),
+  );
+
+const comparisonParametersMatch = (
+  parameters: Readonly<Record<string, unknown>>,
+  run: InvestigationRun,
+): boolean =>
+  Object.keys(parameters).length === 4 &&
+  JSON.stringify(parameters.left_evidence_ids) ===
+    JSON.stringify(run.left_inventory_evidence_ids) &&
+  JSON.stringify(parameters.right_evidence_ids) ===
+    JSON.stringify(run.right_inventory_evidence_ids) &&
+  parameters.offset === 0 &&
+  parameters.limit === run.options.change_limit;
+
+const resultParametersMatch = (
+  parameters: Readonly<Record<string, unknown>>,
+  workspace: InvestigationWorkspace,
+  run: InvestigationRun,
+): boolean =>
+  Object.keys(parameters).length === 5 &&
+  parameters.workspace_id === workspace.workspace_id &&
+  parameters.run_id === run.run_id &&
+  JSON.stringify(parameters.comparison_evidence_ids) ===
+    JSON.stringify([run.comparison_evidence_id]) &&
+  parameters.offset === 0 &&
+  parameters.limit === Math.min(run.options.change_limit, 100);
+
+const providerMatches = (
+  actual: {
+    readonly id: string;
+    readonly name: string;
+    readonly version: string | null;
+  },
+  expected: {
+    readonly id: string;
+    readonly name: string;
+    readonly version: string | null;
+  },
+): boolean =>
+  actual.id === expected.id &&
+  actual.name === expected.name &&
+  actual.version === expected.version;
+
+const valuesMatch = (left: unknown, right: unknown): boolean =>
+  JSON.stringify(left) === JSON.stringify(right);

src/application/ProcessHarness.ts

@@ -243,12 +243,13 @@ const startCaptureRuntime = async (options: {
       renderer,
       started,
     });
-    const stopSampler = startProcessSampler(
-      terminal.pid,
+    const stopSampler = startProcessSampler({
+      rootPid: terminal.pid,
+      runId: options.runId,
       started,
-      scenario.limits.processes,
-      options.samples,
-    );
+      limit: scenario.limits.processes,
+      samples: options.samples,
+    });
     return {
       replay,
       renderer,

src/application/ProcessOwnership.ts

@@ -19,6 +19,7 @@ interface ProcessGroupMember {
   readonly pid: number;
   readonly parentPid: number;
   readonly processGroupId: number;
+  readonly state: string;
   readonly command: string;
 }
 
@@ -30,9 +31,19 @@ export interface ProcessOwnershipHost {
 }
 
 /** Cleanup succeeds only when the group is absent or every member is owned. */
+export interface ProcessOwnershipValidationFailure {
+  readonly pid: number;
+  readonly reason: "environment-unreadable" | "run-token-mismatch";
+}
+
+/** Cleanup outcome with per-member diagnostics when ownership is uncertain. */
 export type ProcessCleanupResult =
   | { readonly cleaned: true; readonly signaled: boolean }
-  | { readonly cleaned: false; readonly reason: string };
+  | {
+      readonly cleaned: false;
+      readonly reason: string;
+      readonly failures?: readonly ProcessOwnershipValidationFailure[];
+    };
 
 /** Token-verified liveness result used by post-root-exit settlement. */
 export type ProcessGroupObservation =
@@ -59,17 +70,18 @@ const systemHost: ProcessOwnershipHost = {
     if (process.platform === "win32") return [];
     const { stdout } = await execFileAsync("ps", [
       "-axo",
-      "pid=,ppid=,pgid=,command=",
+      "pid=,ppid=,pgid=,stat=,command=",
     ]);
     return stdout
       .split("\n")
-      .map((line) => /\s*(\d+)\s+(\d+)\s+(\d+)\s+(.*)/u.exec(line))
+      .map((line) => /\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]),
-        command: match[4] ?? "",
+        state: match[4] ?? "",
+        command: match[5] ?? "",
       }))
       .filter((member) => member.processGroupId === processGroupId);
   },
@@ -92,6 +104,13 @@ const systemHost: ProcessOwnershipHost = {
   },
 };
 
+/** Read the capture run token currently exposed by one live process. */
+export const readProcessRunId = async (
+  pid: number,
+  host: ProcessOwnershipHost = systemHost,
+): Promise<string | undefined> =>
+  (await host.environment(pid)).REA_PROCESS_RUN_ID;
+
 /**
  * Verify run-token ownership before signaling a POSIX process group.
  *
@@ -109,8 +128,11 @@ export const cleanupOwnedProcessGroup = async (
   } catch {
     return { cleaned: false, reason: "process group could not be inspected" };
   }
-  if (members.length === 0) return { cleaned: true, signaled: false };
-  const leader = members.find((member) => member.pid === ownership.leaderPid);
+  const liveMembers = liveProcessGroupMembers(members);
+  if (liveMembers.length === 0) return { cleaned: true, signaled: false };
+  const leader = liveMembers.find(
+    (member) => member.pid === ownership.leaderPid,
+  );
   if (leader !== undefined) {
     if (
       ownership.expectedParentPid !== undefined &&
@@ -129,23 +151,24 @@ export const cleanupOwnedProcessGroup = async (
         reason: "owned launcher command identity did not match",
       };
   }
-  for (const member of members) {
-    let environment: Readonly<Record<string, string>>;
+  const failures: ProcessOwnershipValidationFailure[] = [];
+  for (const member of liveMembers) {
     try {
-      environment = await host.environment(member.pid);
+      const environment = await host.environment(member.pid);
+      if (environment.REA_PROCESS_RUN_ID !== ownership.runId)
+        failures.push({ pid: member.pid, reason: "run-token-mismatch" });
     } catch {
-      return {
-        cleaned: false,
-        reason: "process ownership could not be revalidated",
-      };
-    }
-    if (environment.REA_PROCESS_RUN_ID !== ownership.runId) {
-      return {
-        cleaned: false,
-        reason: "process group contains an unowned or PID-reused process",
-      };
+      failures.push({ pid: member.pid, reason: "environment-unreadable" });
     }
   }
+  if (failures.length > 0)
+    return {
+      cleaned: false,
+      reason: failures.some(({ reason }) => reason === "run-token-mismatch")
+        ? "process group contains an unowned or PID-reused process"
+        : "process ownership could not be revalidated",
+      failures,
+    };
   try {
     host.signalGroup(ownership.processGroupId, "SIGKILL");
   } catch (cause: unknown) {
@@ -171,8 +194,9 @@ export const observeOwnedProcessGroup = async (
       reason: "process group could not be inspected",
     };
   }
-  if (members.length === 0) return { state: "empty" };
-  for (const member of members) {
+  const liveMembers = liveProcessGroupMembers(members);
+  if (liveMembers.length === 0) return { state: "empty" };
+  for (const member of liveMembers) {
     try {
       if (
         (await host.environment(member.pid)).REA_PROCESS_RUN_ID !==
@@ -192,6 +216,11 @@ export const observeOwnedProcessGroup = async (
   return { state: "alive" };
 };
 
+const liveProcessGroupMembers = (
+  members: readonly ProcessGroupMember[],
+): readonly ProcessGroupMember[] =>
+  members.filter(({ state }) => !state.startsWith("Z"));
+
 const commandMatches = (actual: string, expected: string): boolean => {
   const normalizedActual = actual.trim();
   const normalizedExpected = expected.trim();

src/application/ProcessSampling.ts

@@ -2,6 +2,7 @@ import { execFile } from "node:child_process";
 import { readFile, readdir } from "node:fs/promises";
 import { promisify } from "node:util";
 import type { ProcessSample } from "../domain/processCapture.js";
+import { readProcessRunId } from "./ProcessOwnership.js";
 
 const execFileAsync = promisify(execFile);
 const PROC_READ_CONCURRENCY = 64;
@@ -27,6 +28,29 @@ interface SampleProcessContext {
   readonly signal: AbortSignal;
 }
 
+type ProcessIdentitySnapshot = Pick<
+  ProcessRow,
+  "pid" | "parent_pid" | "process_group_id" | "session_id" | "startTime"
+>;
+
+/** Prove that forkpty completed session setup and installed the run token. */
+export const isInitializedPtyRoot = (options: {
+  readonly rootPid: number;
+  readonly expectedRunId: string;
+  readonly before: ProcessIdentitySnapshot;
+  readonly observedRunId: string | undefined;
+  readonly after: ProcessIdentitySnapshot;
+}): boolean =>
+  options.before.pid === options.rootPid &&
+  options.before.process_group_id === options.rootPid &&
+  options.before.session_id === options.rootPid &&
+  options.after.pid === options.rootPid &&
+  options.after.parent_pid === options.before.parent_pid &&
+  options.after.process_group_id === options.rootPid &&
+  options.after.session_id === options.rootPid &&
+  options.after.startTime === options.before.startTime &&
+  options.observedRunId === options.expectedRunId;
+
 const isExpectedProcReadFailure = (cause: unknown): boolean =>
   cause instanceof Error &&
   "code" in cause &&
@@ -305,6 +329,47 @@ const readPsRows = async (
     .sort((left, right) => left.pid - right.pid);
 };
 
+const readRootIdentity = async (
+  rootPid: number,
+  signal: AbortSignal,
+): Promise<ProcessRow | undefined> =>
+  process.platform === "linux"
+    ? readProcessStat(rootPid, signal)
+    : (await readPsRows(signal)).find(({ pid }) => pid === rootPid);
+
+const inspectInitializedPtyRoot = async (
+  rootPid: number,
+  runId: string,
+  signal: AbortSignal,
+): Promise<{ readonly startTime: string | undefined } | undefined> => {
+  const before = await readRootIdentity(rootPid, signal);
+  if (
+    before === undefined ||
+    before.process_group_id !== rootPid ||
+    before.session_id !== rootPid
+  )
+    return undefined;
+  let observedRunId: string | undefined;
+  try {
+    observedRunId = await readProcessRunId(rootPid);
+  } catch {
+    return undefined;
+  }
+  const after = await readRootIdentity(rootPid, signal);
+  if (
+    after === undefined ||
+    !isInitializedPtyRoot({
+      rootPid,
+      expectedRunId: runId,
+      before,
+      observedRunId,
+      after,
+    })
+  )
+    return undefined;
+  return { startTime: after.startTime };
+};
+
 const samplePs = async (
   context: SampleProcessContext,
 ): Promise<readonly ProcessRow[]> => {
@@ -375,31 +440,47 @@ const sampleProcesses = async (
 };
 
 /** Start bounded process-tree sampling and expose an awaited stop. */
-export const startProcessSampler = (
-  rootPid: number,
-  started: number,
-  limit: number,
-  samples: ProcessSample[],
-): (() => Promise<{ readonly partial: boolean }>) => {
+export const startProcessSampler = (options: {
+  readonly rootPid: number;
+  readonly runId: string;
+  readonly started: number;
+  readonly limit: number;
+  readonly samples: ProcessSample[];
+}): (() => Promise<{ readonly partial: boolean }>) => {
+  const { rootPid, runId, started, limit, samples } = options;
   const identities = new Map<number, string>();
   const lastObservations = new Map<number, string>();
   let pending: Promise<void> | undefined;
   let stopped = false;
   let abortCurrent: (() => void) | undefined;
   let partial = false;
+  let rootInitialized = false;
 
   const sample = (): void => {
     if (stopped || pending !== undefined) return;
 
     const controller = new AbortController();
     abortCurrent = () => controller.abort();
-    pending = sampleProcesses({
-      rootPid,
-      elapsedMs: Date.now() - started,
-      limit: limit + 1,
-      identities,
-      signal: controller.signal,
-    })
+    pending = (async () => {
+      if (!rootInitialized) {
+        const identity = await inspectInitializedPtyRoot(
+          rootPid,
+          runId,
+          controller.signal,
+        );
+        if (identity === undefined) return [];
+        if (identity.startTime !== undefined)
+          identities.set(rootPid, identity.startTime);
+        rootInitialized = true;
+      }
+      return sampleProcesses({
+        rootPid,
+        elapsedMs: Date.now() - started,
+        limit: limit + 1,
+        identities,
+        signal: controller.signal,
+      });
+    })()
       .then((values) => {
         for (const value of values) {
           const observation = JSON.stringify({

src/application/ReferenceSourceImport.ts

@@ -1,6 +1,7 @@
 import { isSecretLikePath } from "../domain/referenceSourceClassification.js";
 import {
   createHistoricalSourceGraph,
+  referenceSourceParseFailureKey,
   type HistoricalSourceGraph,
   type HistoricalSourceGraphInput,
 } from "../domain/referenceSourceGraph.js";
@@ -204,18 +205,19 @@ export const importReferenceSource = async (
   if (isAborted(options.signal)) return err(cancelled());
 
   const uniqueRelationships = deduplicateRelationships(relationships);
-  const uniqueFailures = [...parseFailures]
-    .sort((left, right) => {
-      const byPath = byCodePoint(left.path, right.path);
-      if (byPath !== 0) return byPath;
-      return byCodePoint(left.parser, right.parser);
-    })
-    .filter((value, index, array) => {
-      if (index === 0) return true;
-      const previous = array[index - 1];
-      if (previous === undefined) return true;
-      return value.path !== previous.path || value.parser !== previous.parser;
-    });
+  const uniqueFailures = [
+    ...new Map(
+      parseFailures.map((parseFailure) => [
+        referenceSourceParseFailureKey(parseFailure),
+        parseFailure,
+      ]),
+    ).values(),
+  ].sort((left, right) =>
+    byCodePoint(
+      referenceSourceParseFailureKey(left),
+      referenceSourceParseFailureKey(right),
+    ),
+  );
 
   const sortedEntries = [...entries].sort((left, right) =>
     byCodePoint(left.path, right.path),

src/application/Setup.ts

@@ -25,7 +25,10 @@ import { installMacHopper } from "./MacHopper.js";
 import { configureDetectedClients } from "./SetupClients.js";
 import { supportedClients, type SetupClient } from "./SupportedClients.js";
 export type { SetupClient } from "./SupportedClients.js";
-import { installCanonicalSkill } from "./SetupSkill.js";
+import {
+  canonicalSkillInstallationNeeded,
+  installCanonicalSkill,
+} from "./SetupSkill.js";
 import { setupPlan } from "./SetupPlan.js";
 import {
   setupInstallFailure,
@@ -69,6 +72,7 @@ export interface SetupHost {
     hopperPath: string | undefined,
     command: readonly string[],
   ): Promise<ClientConfigurationResult>;
+  skillInstallationNeeded(): Promise<boolean>;
   installSkill(): Promise<"installed" | "unchanged" | "failed">;
   doctor(): Promise<Awaited<ReturnType<typeof runDoctor>>>;
 }
@@ -140,7 +144,13 @@ export const runSetup = async (
   );
   const installHopper = hopperPath === undefined || linuxHopperRepairNeeded;
   const detectedClients = await host.detectedClients();
-  plannedActions = setupPlan(host.platform, installHopper, detectedClients);
+  const installSkill = await host.skillInstallationNeeded();
+  plannedActions = setupPlan(
+    host.platform,
+    installHopper,
+    detectedClients,
+    installSkill,
+  );
   let approved = options.approved;
   let interactiveApproval = false;
   if (!approved && confirm !== undefined && !options.structured) {
@@ -182,12 +192,14 @@ export const runSetup = async (
     appliedActions,
   });
   if (clientFailure !== undefined) return fail(clientFailure);
-  const skill = await host.installSkill();
-  if (skill === "failed")
-    return fail(
-      "REA analysis skill could not be installed or verified. Check permissions for `~/.agents/skills`, then rerun setup.",
-    );
-  if (skill === "installed") appliedActions.push("installed_skill");
+  if (installSkill) {
+    const skill = await host.installSkill();
+    if (skill === "failed")
+      return fail(
+        "REA analysis skill could not be installed or verified. Check permissions for `~/.agents/skills`, then rerun setup.",
+      );
+    if (skill === "installed") appliedActions.push("installed_skill");
+  }
   const doctor = await host.doctor();
   const remediation = finalSetupRemediation(
     host.platform,
@@ -261,6 +273,7 @@ const systemSetupHost = (): SetupHost => {
         : client.format === "toml"
           ? configureTomlClient(client, hopperPath, command)
           : configureJsonClient(client, hopperPath, command),
+    skillInstallationNeeded: () => canonicalSkillInstallationNeeded(homedir()),
     installSkill: () => installCanonicalSkill(homedir()),
     doctor: () => runDoctor(undefined, doctorHost),
   };

src/application/SetupClients.ts

@@ -14,7 +14,7 @@ const failedConfigurationMessage = (
   return "Agent configuration could not be verified after writing. Repair the configuration file or restore its `.rea.backup`, then rerun setup.";
 };
 
-/** Configure each detected agent, stopping after the first failed transaction. */
+/** Configure every detected agent and report all failed transaction classes. */
 export const configureDetectedClients = async (options: {
   readonly host: SetupHost;
   readonly detectedClients: readonly SetupClient[];
@@ -23,6 +23,7 @@ export const configureDetectedClients = async (options: {
   readonly clients: Record<string, ClientConfigurationResult>;
   readonly appliedActions: string[];
 }): Promise<string | undefined> => {
+  const failures = new Set<"backup" | "write" | "readback">();
   for (const client of options.detectedClients) {
     const result = await options.host.configureClient(
       client,
@@ -30,10 +31,11 @@ export const configureDetectedClients = async (options: {
       options.command,
     );
     options.clients[client.name] = result;
-    if (result.status === "failed")
-      return failedConfigurationMessage(result.reason);
+    if (result.status === "failed") failures.add(result.reason);
     if (result.status === "configured")
       options.appliedActions.push(`configured_${client.name}`);
   }
-  return undefined;
+  return failures.size === 0
+    ? undefined
+    : [...failures].map(failedConfigurationMessage).join(" ");
 };

src/application/SetupPlan.ts

@@ -5,6 +5,7 @@ export const setupPlan = (
   platform: NodeJS.Platform,
   installHopper: boolean,
   clients: readonly SetupClient[],
+  installSkill: boolean,
 ): readonly SetupAction[] => [
   ...(installHopper
     ? [
@@ -32,10 +33,14 @@ export const setupPlan = (
         external: false,
       }),
     ),
-  {
-    kind: "install_skill",
-    target: "~/.agents/skills/rea-analysis/SKILL.md",
-    detail: "Install or update the bundled REA analysis skill.",
-    external: false,
-  },
+  ...(installSkill
+    ? [
+        {
+          kind: "install_skill" as const,
+          target: "~/.agents/skills/rea-analysis/SKILL.md",
+          detail: "Install or update the bundled REA analysis skill.",
+          external: false,
+        },
+      ]
+    : []),
 ];

src/application/SetupSkill.ts

@@ -4,26 +4,43 @@ import writeFileAtomic from "write-file-atomic";
 
 import { PRODUCT_IDENTITY } from "../identity.js";
 
+const canonicalSkillDestination = (home: string): string =>
+  join(home, ".agents/skills", PRODUCT_IDENTITY.skillName, "SKILL.md");
+
+const readCanonicalSkill = (): Promise<string> =>
+  readFile(
+    new URL(
+      `../../skills/${PRODUCT_IDENTITY.skillName}/SKILL.md`,
+      import.meta.url,
+    ),
+    "utf8",
+  );
+
+/** Determine whether setup would need to install or update the canonical skill. */
+export const canonicalSkillInstallationNeeded = async (
+  home: string,
+): Promise<boolean> => {
+  try {
+    const [canonical, installed] = await Promise.all([
+      readCanonicalSkill(),
+      readFile(canonicalSkillDestination(home), "utf8").catch(() => undefined),
+    ]);
+    return installed !== canonical;
+  } catch {
+    // Disclose the action when setup cannot prove the installed copy is aligned.
+    return true;
+  }
+};
+
 /** Transactionally install or upgrade the versioned canonical REA skill. */
 export const installCanonicalSkill = async (
   home: string,
 ): Promise<"installed" | "unchanged" | "failed"> => {
-  const destination = join(
-    home,
-    ".agents/skills",
-    PRODUCT_IDENTITY.skillName,
-    "SKILL.md",
-  );
+  const destination = canonicalSkillDestination(home);
   const backup = `${destination}.rea.backup`;
   let original: string | undefined;
   try {
-    const content = await readFile(
-      new URL(
-        `../../skills/${PRODUCT_IDENTITY.skillName}/SKILL.md`,
-        import.meta.url,
-      ),
-      "utf8",
-    );
+    const content = await readCanonicalSkill();
     original = await readFile(destination, "utf8").catch(() => undefined);
     if (original === content) return "unchanged";
     await mkdir(dirname(destination), { recursive: true });

src/application/Upgrade.ts

@@ -194,6 +194,8 @@ const runCommand = (
 ): Promise<boolean> =>
   new Promise((resolveResult) => {
     const child = spawn(command, [...arguments_], {
+      // Reserve parent stdout for Incur's structured result. Array positions
+      // are child fds 0/1/2, so npm stdout and stderr both reach parent stderr.
       stdio:
         output === "human" ? "inherit" : ["inherit", process.stderr, "inherit"],
     });

src/browser/CdpBrowserProvider.ts

@@ -328,6 +328,7 @@ export class CdpBrowserProvider implements BrowserObservationPort {
       return await capturePage({
         connection: targetSession.connection,
         sessionId: targetSession.sessionId,
+        operation,
         discovery,
         target,
         input,

src/browser/CdpCaptureValues.ts

@@ -1,6 +1,7 @@
 import {
   AnalysisCancelledError,
   BrowserObservationError,
+  type BrowserObservationOperation,
 } from "../domain/errors.js";
 import { sanitizeBrowserUrl } from "../domain/browserObservation.js";
 import { createWebTextArtifact } from "../domain/webContentArtifact.js";
@@ -74,11 +75,11 @@ export const sourceExcluded = (
 
 export const delayWithCancellation = async (
   durationMs: number,
+  operation: BrowserObservationOperation,
   signal?: AbortSignal,
 ): Promise<void> => {
   if (durationMs === 0) return;
-  if (signal?.aborted === true)
-    throw new AnalysisCancelledError("inspect_web_page");
+  if (signal?.aborted === true) throw new AnalysisCancelledError(operation);
   await new Promise<void>((resolve, reject) => {
     const timer = setTimeout(() => {
       signal?.removeEventListener("abort", onAbort);
@@ -87,7 +88,7 @@ export const delayWithCancellation = async (
     const onAbort = (): void => {
       clearTimeout(timer);
       signal?.removeEventListener("abort", onAbort);
-      reject(new AnalysisCancelledError("inspect_web_page"));
+      reject(new AnalysisCancelledError(operation));
     };
     signal?.addEventListener("abort", onAbort, { once: true });
     if (signal?.aborted === true) onAbort();

src/browser/CdpConnection.ts

@@ -5,6 +5,7 @@ import {
   AnalysisError,
   AnalysisTimeoutError,
   BrowserObservationError,
+  type BrowserObservationOperation,
 } from "../domain/errors.js";
 
 export interface CdpEvent {
@@ -25,34 +26,38 @@ const COMMAND_TIMEOUT_MS = 5_000;
 const MAX_PAYLOAD_BYTES = 16 * 1_024 * 1_024;
 const MAX_PENDING_COMMANDS = 128;
 
-/** Correlated, bounded JSON-RPC transport for a browser-level CDP socket. */
+/** Correlated, bounded JSON-RPC transport for one CDP target operation. */
 export class CdpConnection {
   readonly #pending = new Map<number, PendingCommand>();
   readonly #listeners = new Set<(event: CdpEvent) => void>();
+  readonly #disconnectListeners = new Set<() => void>();
   #nextId = 1;
   #closed = false;
   #protocolFailed = false;
 
-  private constructor(private readonly socket: WebSocket) {
+  private constructor(
+    private readonly socket: WebSocket,
+    private readonly operation: BrowserObservationOperation,
+  ) {
     socket.on("message", (data) => this.#receive(data));
-    socket.on("close", () => this.#failPending("disconnected"));
-    socket.on("error", () => this.#failPending("disconnected"));
+    socket.on("close", () => this.#disconnect());
+    socket.on("error", () => this.#disconnect());
   }
 
-  /** Connect to one already-validated loopback browser WebSocket. */
+  /** Connect to one already-validated loopback CDP WebSocket. */
   static async connect(
     url: string,
+    operation: BrowserObservationOperation,
     signal?: AbortSignal,
   ): Promise<CdpConnection> {
-    if (signal?.aborted === true)
-      throw new AnalysisCancelledError("inspect_web_page");
+    if (signal?.aborted === true) throw new AnalysisCancelledError(operation);
     const socket = new WebSocket(url, {
       handshakeTimeout: CONNECT_TIMEOUT_MS,
       maxPayload: MAX_PAYLOAD_BYTES,
       perMessageDeflate: false,
     });
-    await waitForOpen(socket, signal);
-    return new CdpConnection(socket);
+    await waitForOpen(socket, operation, signal);
+    return new CdpConnection(socket, operation);
   }
 
   /** Subscribe to validated CDP event envelopes. */
@@ -61,6 +66,16 @@ export class CdpConnection {
     return () => this.#listeners.delete(listener);
   }
 
+  /** Subscribe to an unexpected transport loss while an operation is active. */
+  onDisconnect(listener: () => void): () => void {
+    if (this.#closed) {
+      listener();
+      return () => undefined;
+    }
+    this.#disconnectListeners.add(listener);
+    return () => this.#disconnectListeners.delete(listener);
+  }
+
   /** Execute one bounded command, optionally within a flat target session. */
   async send(
     method: string,
@@ -69,13 +84,13 @@ export class CdpConnection {
     signal?: AbortSignal,
   ): Promise<unknown> {
     if (this.#protocolFailed)
-      throw new BrowserObservationError("inspect_web_page", "protocol_error");
+      throw new BrowserObservationError(this.operation, "protocol_error");
     if (this.#closed || this.socket.readyState !== WebSocket.OPEN)
-      throw new BrowserObservationError("inspect_web_page", "disconnected");
+      throw new BrowserObservationError(this.operation, "disconnected");
     if (this.#pending.size >= MAX_PENDING_COMMANDS)
-      throw new BrowserObservationError("inspect_web_page", "payload_limit");
+      throw new BrowserObservationError(this.operation, "payload_limit");
     if (signal?.aborted === true)
-      throw new AnalysisCancelledError("inspect_web_page");
+      throw new AnalysisCancelledError(this.operation);
     const id = this.#nextId;
     this.#nextId += 1;
     return await new Promise((resolve, reject) => {
@@ -85,15 +100,13 @@ export class CdpConnection {
         clearTimeout(pending.timer);
         pending.removeAbort();
         this.#pending.delete(id);
-        reject(new AnalysisCancelledError("inspect_web_page"));
+        reject(new AnalysisCancelledError(this.operation));
       };
       signal?.addEventListener("abort", onAbort, { once: true });
       const timer = setTimeout(() => {
         signal?.removeEventListener("abort", onAbort);
         this.#pending.delete(id);
-        reject(
-          new AnalysisTimeoutError("inspect_web_page", COMMAND_TIMEOUT_MS),
-        );
+        reject(new AnalysisTimeoutError(this.operation, COMMAND_TIMEOUT_MS));
       }, COMMAND_TIMEOUT_MS);
       this.#pending.set(id, {
         resolve,
@@ -114,7 +127,7 @@ export class CdpConnection {
           if (pending === undefined) return;
           this.#complete(id, pending);
           reject(
-            new BrowserObservationError("inspect_web_page", "disconnected", {
+            new BrowserObservationError(this.operation, "disconnected", {
               cause: error,
             }),
           );
@@ -191,7 +204,7 @@ export class CdpConnection {
     this.#complete(id, pending);
     if ("error" in message) {
       pending.reject(
-        new BrowserObservationError("inspect_web_page", "protocol_error"),
+        new BrowserObservationError(this.operation, "protocol_error"),
       );
       return;
     }
@@ -209,9 +222,17 @@ export class CdpConnection {
     else this.#protocolFailed = true;
     for (const [id, pending] of this.#pending) {
       this.#complete(id, pending);
-      pending.reject(new BrowserObservationError("inspect_web_page", reason));
+      pending.reject(new BrowserObservationError(this.operation, reason));
     }
   }
+
+  #disconnect(): void {
+    const wasClosed = this.#closed;
+    this.#failPending("disconnected");
+    if (wasClosed) return;
+    for (const listener of this.#disconnectListeners) listener();
+    this.#disconnectListeners.clear();
+  }
 }
 
 const rawText = (data: RawData): string =>
@@ -226,13 +247,14 @@ const isRecord = (value: unknown): value is Record<string, unknown> =>
 
 const waitForOpen = async (
   socket: WebSocket,
+  operation: BrowserObservationOperation,
   signal?: AbortSignal,
 ): Promise<void> =>
   await new Promise((resolve, reject) => {
     const timer = setTimeout(() => {
       cleanup();
       terminateSocket(socket);
-      reject(new AnalysisTimeoutError("inspect_web_page", CONNECT_TIMEOUT_MS));
+      reject(new AnalysisTimeoutError(operation, CONNECT_TIMEOUT_MS));
     }, CONNECT_TIMEOUT_MS);
     const onOpen = (): void => {
       cleanup();
@@ -242,17 +264,15 @@ const waitForOpen = async (
       cleanup();
       reject(
         signal?.aborted === true
-          ? new AnalysisCancelledError("inspect_web_page")
-          : new BrowserObservationError(
-              "inspect_web_page",
-              "endpoint_unreachable",
-              { cause },
-            ),
+          ? new AnalysisCancelledError(operation)
+          : new BrowserObservationError(operation, "endpoint_unreachable", {
+              cause,
+            }),
       );
     };
     const onAbort = (): void => {
       terminateSocket(socket);
-      onFailure(new AnalysisCancelledError("inspect_web_page"));
+      onFailure(new AnalysisCancelledError(operation));
     };
     const cleanup = (): void => {
       clearTimeout(timer);

src/browser/CdpElectronInspection.ts

@@ -95,7 +95,11 @@ export const inspectCdpElectronPage = async (
       context.sessionId,
       context.signal,
     );
-    await delayWithCancellation(context.input.observation_ms, context.signal);
+    await delayWithCancellation(
+      context.input.observation_ms,
+      "inspect_electron_page",
+      context.signal,
+    );
     await report(context.progress, 2, "Capturing Electron structure");
     const resources = await captureResources(context, roots, completeness);
     const dom = await captureDom(context, roots, completeness);

src/browser/CdpElectronProvider.ts

@@ -54,7 +54,7 @@ export class CdpElectronProvider implements ElectronObservationPort {
       const roots = await canonicalElectronRoots(input.allowed_file_roots);
       const discovery = await discoverCdpEndpoint(
         input.cdp_endpoint,
-        "list_browser_targets",
+        "list_electron_targets",
         options.signal,
       );
       const allowed = [];

src/browser/CdpObservationSession.ts

@@ -3,7 +3,10 @@ import type {
   ObserveWebSessionInput,
   WebObservationSession,
 } from "../domain/browserSession.js";
-import { BrowserObservationError } from "../domain/errors.js";
+import {
+  AnalysisCancelledError,
+  BrowserObservationError,
+} from "../domain/errors.js";
 import type { CdpEndpointDiscovery, CdpEndpointTarget } from "./CdpEndpoint.js";
 import { CdpConnection, type CdpEvent } from "./CdpConnection.js";
 import { CdpCaptureCompleteness } from "./CdpCaptureCompleteness.js";
@@ -48,8 +51,12 @@ export const observeCdpSession = async (
     initialUrl,
   );
   const removeListener = context.connection.onEvent((event) => {
-    if (event.sessionId === context.sessionId) capture.ingest(event);
+    if (observationEventMatches(event, context.sessionId))
+      capture.ingest(event);
   });
+  const removeDisconnectListener = context.connection.onDisconnect(() =>
+    capture.targetTerminated(),
+  );
   try {
     await context.connection.send(
       "Page.enable",
@@ -115,6 +122,7 @@ export const observeCdpSession = async (
     };
   } finally {
     removeListener();
+    removeDisconnectListener();
   }
 };
 
@@ -162,8 +170,7 @@ class TimelineCapture {
         break;
       case "Inspector.targetCrashed":
       case "Target.detachedFromTarget":
-        this.#add("target_terminated", params, null, null, "target_terminated");
-        this.end("target_terminated");
+        this.targetTerminated();
         break;
     }
   }
@@ -181,6 +188,12 @@ class TimelineCapture {
     this.#listeners.clear();
   }
 
+  targetTerminated(): void {
+    if (this.#endReason !== undefined) return;
+    this.#add("target_terminated", {}, null, null, "target_terminated");
+    this.end("target_terminated");
+  }
+
   setFinalUrl(rawUrl: string): void {
     const destination = scopedUrl(rawUrl, this.allowedOrigins);
     this.finalUrl = destination.scope === "approved" ? destination.url : null;
@@ -300,6 +313,18 @@ class TimelineCapture {
   }
 }
 
+const observationEventMatches = (
+  event: CdpEvent,
+  sessionId: string | undefined,
+): boolean => {
+  if (event.method !== "Target.detachedFromTarget")
+    return event.sessionId === sessionId;
+  return (
+    sessionId !== undefined &&
+    stringValue(recordValue(event.params)?.sessionId) === sessionId
+  );
+};
+
 const waitForWindow = async (
   durationMs: number,
   capture: TimelineCapture,
@@ -321,7 +346,7 @@ const waitForWindow = async (
       settled = true;
       clearTimeout(timer);
       removeEnd();
-      reject(signal?.reason ?? new Error("browser observation cancelled"));
+      reject(new AnalysisCancelledError("observe_web_session"));
     };
     const timer = setTimeout(() => finish("window_elapsed"), durationMs);
     removeEnd = capture.onEnd(finish);
@@ -347,7 +372,7 @@ const authorizedFrame = async (
         "inspect_web_page",
         "target_not_allowed",
       );
-    await delayWithCancellation(25, context.signal);
+    await delayWithCancellation(25, "observe_web_session", context.signal);
   }
   throw new BrowserObservationError("inspect_web_page", "target_not_allowed");
 };

src/browser/CdpPageCapture.ts

@@ -3,7 +3,10 @@ import type {
   WebPageInspection,
 } from "../domain/browserObservation.js";
 import type { ProgressReporter } from "../application/ProgressReporter.js";
-import { BrowserObservationError } from "../domain/errors.js";
+import {
+  BrowserObservationError,
+  type BrowserObservationOperation,
+} from "../domain/errors.js";
 import {
   reconcileCapturedWebScript,
   stableWebResources,
@@ -38,6 +41,10 @@ import type { WebSourceMapRequest } from "./WebSourceMapFetcher.js";
 interface CaptureContext {
   readonly connection: CdpConnection;
   readonly sessionId: string | undefined;
+  readonly operation: Extract<
+    BrowserObservationOperation,
+    "inspect_web_page" | "analyze_web_bundle"
+  >;
   readonly discovery: CdpEndpointDiscovery;
   readonly target: CdpEndpointTarget;
   readonly input: InspectWebPageInput;
@@ -225,7 +232,11 @@ const authorizeObservationWindow = async (
   events.beginAuthorizedFrame(mainFrame.frame_id);
   await enableObservationDomains(connection, sessionId, signal);
   await report(context.progress, 2, "Observing page events");
-  await delayWithCancellation(context.input.observation_ms, signal);
+  await delayWithCancellation(
+    context.input.observation_ms,
+    context.operation,
+    signal,
+  );
   if (events.originViolation)
     throw new BrowserObservationError("inspect_web_page", "target_not_allowed");
 };
@@ -323,7 +334,7 @@ const authorizedFrameTree = async (
         "inspect_web_page",
         "target_not_allowed",
       );
-    await delayWithCancellation(25, context.signal);
+    await delayWithCancellation(25, context.operation, context.signal);
   }
   throw new BrowserObservationError("inspect_web_page", "target_not_allowed");
 };

src/browser/CdpTargetSession.ts

@@ -23,7 +23,11 @@ export const openCdpTargetSession = async (
   signal?: AbortSignal,
 ): Promise<CdpTargetSession> => {
   const webSocket = cdpTargetWebSocket(discovery, target, operation);
-  const connection = await CdpConnection.connect(webSocket.url, signal);
+  const connection = await CdpConnection.connect(
+    webSocket.url,
+    operation,
+    signal,
+  );
   if (webSocket.scope === "page") return { connection, sessionId: undefined };
   try {
     const attached = await connection.send(

src/browser/CdpWebMcpDiscovery.ts

@@ -96,6 +96,7 @@ export const discoverWebMcp = async (
       // CDP sends the enable response before the required toolsAdded replay.
       await delayWithCancellation(
         Math.max(context.input.observation_ms, 25),
+        "discover_webmcp_tools",
         context.signal,
       );
     await assertStableAuthorizedFrame(context, initialUrl, origins);

src/cli.ts

@@ -160,7 +160,9 @@ const registerSetupCommands = (
       installHopper: z
         .boolean()
         .default(false)
-        .describe("Also approve Hopper installation with --yes"),
+        .describe(
+          "Approve Hopper installation when missing or repair is needed (requires --yes)",
+        ),
     }),
     alias: { yes: "y", installHopper: "install-hopper" },
     run: ({ options, formatExplicit }) =>

src/cliInvestigationCommands.ts

@@ -18,6 +18,11 @@ const investigationOptionsSchema = z.object({
     .describe("Approve persistent workspace writes"),
   workspaceName: z.string().trim().min(1).max(200).default("default"),
   expectedRevision: z.number().int().min(1).optional(),
+  replayRunId: z
+    .string()
+    .regex(/^run_[a-f0-9]{64}$/u)
+    .optional()
+    .describe("Replay one verified complete workspace run without rescanning"),
   maxEntries: z.number().int().min(1).max(50_000).default(10_000),
   maxTotalBytes: z
     .number()
@@ -55,6 +60,7 @@ export const registerInvestigationCommands = (
     alias: {
       workspaceName: "workspace-name",
       expectedRevision: "expected-revision",
+      replayRunId: "replay-run-id",
       maxEntries: "max-entries",
       maxTotalBytes: "max-total-bytes",
       maxEntryBytes: "max-entry-bytes",
@@ -99,13 +105,6 @@ const runInvestigation = async (
     },
   );
   if (!workspaceAuthorization.ok) return cliError(workspaceAuthorization.error);
-  const inputAuthorization = await authorizeRootPermission(authority.value, {
-    capability: "investigation_input",
-    roots: [args.leftPath, args.rightPath],
-    access: "read",
-    operation: "investigate_versions",
-  });
-  if (!inputAuthorization.ok) return cliError(inputAuthorization.error);
   const investigated = await runCrossVersionInvestigation(
     {
       approved: true,
@@ -114,6 +113,9 @@ const runInvestigation = async (
       ...(options.expectedRevision === undefined
         ? {}
         : { expected_workspace_revision: options.expectedRevision }),
+      ...(options.replayRunId === undefined
+        ? {}
+        : { replay_run_id: options.replayRunId }),
       left_path: args.leftPath,
       right_path: args.rightPath,
       integrity_policy: options.integrityPolicy,
@@ -134,6 +136,13 @@ const runInvestigation = async (
     {
       inputRoots: config.value.investigationInputRoots,
       integrityContinueEnabled: config.value.artifactIntegrityContinueEnabled,
+      authorizeInputRead: () =>
+        authorizeRootPermission(authority.value, {
+          capability: "investigation_input",
+          roots: [args.leftPath, args.rightPath],
+          access: "read",
+          operation: "investigate_versions",
+        }),
       authorizeWorkspaceWrite: workspaceAuthorization.value.authorizeWrite,
     },
   );

src/cliPolicyCommands.ts

@@ -1,4 +1,5 @@
 import { Cli, z } from "incur";
+import { createInterface } from "node:readline/promises";
 
 import { loadConfiguredPermissionAuthority } from "./application/PermissionConfiguration.js";
 import {
@@ -49,9 +50,13 @@ export const registerPolicyCommands = (
       network: z.enum(["none", "loopback", "external"]).default("none"),
       mount: z.boolean().default(false),
       write: z.boolean().default(false),
+      yes: z
+        .boolean()
+        .default(false)
+        .describe("Confirm a destructive policy revocation without prompting"),
     }),
-    alias: { environmentNames: "environment-names" },
-    run: ({ args, options }) =>
+    alias: { environmentNames: "environment-names", yes: "y" },
+    run: ({ args, options, formatExplicit }) =>
       logCliCommand(logger, "policy", async () => {
         const config = parseConfig(process.env);
         if (!config.ok) return failure(config.error);
@@ -76,6 +81,22 @@ export const registerPolicyCommands = (
             permissionProjectStore === undefined
           )
             return { error: "Project policy is not configured" };
+          if (!options.yes) {
+            if (formatExplicit || process.stdin.isTTY !== true)
+              return {
+                error: "ConfirmationRequired",
+                message: "Policy grant revocation requires confirmation",
+                grant_id: args.value,
+                remediation:
+                  "Verify the grant ID, then rerun the same command with --yes.",
+              };
+            if (!(await confirmRevocation(args.value)))
+              return {
+                error: "Cancelled",
+                message: "Policy grant revocation was cancelled",
+                grant_id: args.value,
+              };
+          }
           const revoked = await revokeProjectPermissionGrant(
             permissionProjectStore,
             permissionProjectRoot,
@@ -100,6 +121,23 @@ export const registerPolicyCommands = (
   });
 };
 
+const confirmRevocation = async (grantId: string): Promise<boolean> => {
+  const prompt = createInterface({
+    input: process.stdin,
+    output: process.stdout,
+  });
+  try {
+    const answer = (
+      await prompt.question(`Revoke policy grant "${grantId}"? [y/N] `)
+    )
+      .trim()
+      .toLowerCase();
+    return answer === "y" || answer === "yes";
+  } finally {
+    prompt.close();
+  }
+};
+
 const explain = async (
   config: AppConfig,
   capability: PermissionCapability,

src/domain/investigationWorkspace.ts

@@ -59,6 +59,10 @@ export const crossVersionInvestigationInputSchema = z
     workspace_path: z.string().min(1).max(4_096),
     workspace_name: z.string().trim().min(1).max(200).default("default"),
     expected_workspace_revision: z.number().int().min(1).optional(),
+    replay_run_id: z
+      .string()
+      .regex(/^run_[a-f0-9]{64}$/u)
+      .optional(),
     left_path: z.string().min(1).max(4_096),
     right_path: z.string().min(1).max(4_096),
     integrity_policy: z.enum(["fail", "record-and-continue"]).default("fail"),

src/domain/referenceSourceGraph.ts

@@ -128,6 +128,11 @@ const parseFailureSchema = z.strictObject({
   reason: boundedTextSchema,
 });
 
+/** Stable identity for one distinct reference-source parse failure. */
+export const referenceSourceParseFailureKey = (
+  failure: z.infer<typeof parseFailureSchema>,
+): string => JSON.stringify([failure.path, failure.parser, failure.reason]);
+
 const exclusionSchema = z.strictObject({
   path: relativePathSchema,
   reason: z.enum([
@@ -400,7 +405,7 @@ function checkGraphInvariants(
     context,
   );
   checkSortedUnique(
-    graph.parse_failures.map(({ path, parser }) => `${path}\u0000${parser}`),
+    graph.parse_failures.map(referenceSourceParseFailureKey),
     "parse_failures",
     context,
   );

src/hopper/BridgeLauncher.ts

@@ -40,15 +40,25 @@ export interface BridgeLauncher {
   ): Promise<Result<BridgeLaunch, HopperStartError | HopperCancelledError>>;
 }
 
-export interface HopperApplicationLauncherOptions {
+interface SharedHopperApplicationLauncherOptions {
   readonly launcherPath: string;
   readonly targetPath: string;
   readonly targetKind: "executable" | "database";
   readonly loaderArgs: readonly string[];
   readonly bridgeScriptPath: string;
-  readonly demoHelperPath?: string;
 }
 
+/** Explicit launcher contract; the Linux adapter verifies its pinned Hopper build before execution. */
+export type HopperApplicationLauncherOptions =
+  | (SharedHopperApplicationLauncherOptions & {
+      readonly launchMode: "native";
+      readonly demoHelperPath?: never;
+    })
+  | (SharedHopperApplicationLauncherOptions & {
+      readonly launchMode: "verified_linux_demo";
+      readonly demoHelperPath: string;
+    });
+
 /**
  * Launches Hopper through its documented CLI and injects only REA's owned bridge.
  *
@@ -186,10 +196,13 @@ const linuxDemoLaunch = (
   };
 };
 
-const usesLinuxDemo = (options: HopperApplicationLauncherOptions): boolean =>
-  process.platform === "linux" &&
-  basename(options.launcherPath) === "Hopper" &&
-  options.demoHelperPath !== undefined;
+/** Select the version-pinned adapter from the caller's explicit launch mode. */
+export const usesLinuxDemo = (
+  options: HopperApplicationLauncherOptions,
+): options is HopperApplicationLauncherOptions & {
+  readonly launchMode: "verified_linux_demo";
+  readonly demoHelperPath: string;
+} => options.launchMode === "verified_linux_demo";
 
 const spawnLauncher = async (
   command: string,

src/hopper/HopperProvider.ts

@@ -114,9 +114,14 @@ export class HopperProvider implements AnalysisProvider {
         bridgeScriptPath: fileURLToPath(
           new URL("../../bridge/hopper_bridge.py", import.meta.url),
         ),
-        demoHelperPath: fileURLToPath(
-          new URL("../../scripts/hopper-demo-x11.py", import.meta.url),
-        ),
+        ...(process.platform === "linux"
+          ? {
+              launchMode: "verified_linux_demo" as const,
+              demoHelperPath: fileURLToPath(
+                new URL("../../scripts/hopper-demo-x11.py", import.meta.url),
+              ),
+            }
+          : { launchMode: "native" as const }),
       }),
       logger: this.logger.child({ layer: "bridge" }),
     });

src/main.ts

@@ -33,7 +33,7 @@ interface RuntimeDependencies {
   readonly serve: typeof serveStdio;
   readonly writeStderr: (text: string) => void;
   readonly setExitCode: (code: number) => void;
-  readonly registerShutdown: (handler: () => void) => void;
+  readonly registerShutdown: (handler: () => void) => () => void;
   readonly registerReload?: (handler: () => void) => () => void;
 }
 
@@ -49,6 +49,15 @@ const runtimeDependencies = (): RuntimeDependencies => ({
     process.once("SIGTERM", handler);
     process.stdin.once("end", handler);
     process.stdin.once("close", handler);
+    let registered = true;
+    return () => {
+      if (!registered) return;
+      registered = false;
+      process.off("SIGINT", handler);
+      process.off("SIGTERM", handler);
+      process.stdin.off("end", handler);
+      process.stdin.off("close", handler);
+    };
   },
   registerReload: (handler) => {
     process.on("SIGHUP", handler);
@@ -241,9 +250,11 @@ export const run = async (
       })();
     }) ?? (() => undefined);
 
+  let unregisterShutdown = (): void => undefined;
   let shutdownPromise: Promise<void> | undefined;
   const shutdown = (): Promise<void> => {
     shutdownPromise ??= (async () => {
+      unregisterShutdown();
       unregisterReload();
       await handle.close();
       await session.close();
@@ -259,7 +270,8 @@ export const run = async (
     });
   };
 
-  dependencies.registerShutdown(requestShutdown);
+  unregisterShutdown = dependencies.registerShutdown(requestShutdown);
+  if (shutdownPromise !== undefined) unregisterShutdown();
   return 0;
 };
 

src/server/registerInvestigationTools.ts

@@ -19,7 +19,10 @@ import {
 } from "../domain/changedBehavior.js";
 import { createEvidence, type Evidence } from "../domain/evidence.js";
 import type { EvidenceFilePolicy } from "../domain/evidenceBundle.js";
-import { EvidenceIntegrityError } from "../domain/errors.js";
+import {
+  EvidenceIntegrityError,
+  type AnalysisError,
+} from "../domain/errors.js";
 import { jsonValueSchema } from "../domain/jsonValue.js";
 import { err, ok, type Result } from "../domain/result.js";
 import {
@@ -93,14 +96,19 @@ const registerChangedBehavior = (
     contractOptions(contract),
     async (input, context) => {
       const parsed = changedBehaviorInputSchema.parse(input);
-      if (parsed.investigation_run !== undefined) {
+      const investigationRun = parsed.investigation_run;
+      if (investigationRun !== undefined) {
         const progress = mcpProgressReporter(context);
         let workspaceAuthorization: DeferredFileWriteAuthorization | undefined;
+        let authorizeInputRead:
+          | (() => Promise<Result<null, AnalysisError>>)
+          | undefined;
         if (policies.permissionAuthority !== undefined) {
+          const authority = policies.permissionAuthority;
           const authorizedWorkspace = await authorizeFileReadWithDeferredWrite(
-            policies.permissionAuthority,
+            authority,
             {
-              path: parsed.investigation_run.workspace_path,
+              path: investigationRun.workspace_path,
               readCapability: "investigation_workspace_read",
               writeCapability: "investigation_workspace_write",
               operation: contract.name,
@@ -109,23 +117,16 @@ const registerChangedBehavior = (
           if (!authorizedWorkspace.ok)
             return toCallToolResult(authorizedWorkspace, contract);
           workspaceAuthorization = authorizedWorkspace.value;
-          const authorizedInput = await authorizeRootPermission(
-            policies.permissionAuthority,
-            {
+          authorizeInputRead = () =>
+            authorizeRootPermission(authority, {
               capability: "investigation_input",
-              roots: [
-                parsed.investigation_run.left_path,
-                parsed.investigation_run.right_path,
-              ],
+              roots: [investigationRun.left_path, investigationRun.right_path],
               access: "read",
               operation: contract.name,
-            },
-          );
-          if (!authorizedInput.ok)
-            return toCallToolResult(authorizedInput, contract);
+            });
         }
         const investigated = await runCrossVersionInvestigation(
-          parsed.investigation_run,
+          investigationRun,
           policies.evidenceFiles,
           {
             ...investigationExecution(
@@ -141,6 +142,7 @@ const registerChangedBehavior = (
                   authorizeWorkspaceWrite:
                     workspaceAuthorization.authorizeWrite,
                 }),
+            ...(authorizeInputRead === undefined ? {} : { authorizeInputRead }),
           },
         );
         if (!investigated.ok) return toCallToolResult(investigated, contract);

tests/bridgeLauncher.test.ts

@@ -0,0 +1,85 @@
+import { execFile } from "node:child_process";
+import { access, chmod, mkdtemp, rm, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { promisify } from "node:util";
+import { fileURLToPath } from "node:url";
+
+import { describe, expect, it } from "vitest";
+
+import {
+  type HopperApplicationLauncherOptions,
+  usesLinuxDemo,
+} from "../src/hopper/BridgeLauncher.js";
+
+const execFileAsync = promisify(execFile);
+const demoHelperPath = fileURLToPath(
+  new URL("../scripts/hopper-demo-x11.py", import.meta.url),
+);
+
+const options = (launcherPath: string): HopperApplicationLauncherOptions => ({
+  launcherPath,
+  targetPath: "/target",
+  targetKind: "executable",
+  loaderArgs: [],
+  bridgeScriptPath: "/rea/hopper_bridge.py",
+  launchMode: "verified_linux_demo",
+  demoHelperPath: "/rea/hopper-demo-x11.py",
+});
+
+describe("Hopper bridge launcher selection", () => {
+  it.each([
+    "/opt/hopper/bin/Hopper",
+    "/usr/local/bin/hopper",
+    "/workspace/bin/hopper-wrapper",
+  ])(
+    "routes launcher spelling %s through the explicitly selected pinned adapter",
+    (path) => {
+      expect(usesLinuxDemo(options(path))).toBe(true);
+    },
+  );
+
+  it("does not infer demo behavior from a native launcher's basename", () => {
+    expect(
+      usesLinuxDemo({
+        launcherPath: "/opt/hopper/bin/Hopper",
+        targetPath: "/target",
+        targetKind: "executable",
+        loaderArgs: [],
+        bridgeScriptPath: "/rea/hopper_bridge.py",
+        launchMode: "native",
+      }),
+    ).toBe(false);
+  });
+
+  it("rejects an unpinned wrapper before executing it", async () => {
+    const directory = await mkdtemp(join(tmpdir(), "rea-hopper-wrapper-"));
+    const wrapper = join(directory, "hopper-wrapper");
+    const marker = join(directory, "executed");
+    try {
+      await writeFile(wrapper, `#!/bin/sh\ntouch ${JSON.stringify(marker)}\n`);
+      await chmod(wrapper, 0o700);
+      await expect(
+        execFileAsync(
+          "python3",
+          [
+            demoHelperPath,
+            "--hopper",
+            wrapper,
+            "--socket",
+            join(directory, "bridge.sock"),
+            "--",
+            wrapper,
+          ],
+          { timeout: 3_000 },
+        ),
+      ).rejects.toMatchObject({
+        code: 72,
+        stderr: expect.stringContaining("unsupported Hopper binary"),
+      });
+      await expect(access(marker)).rejects.toMatchObject({ code: "ENOENT" });
+    } finally {
+      await rm(directory, { recursive: true, force: true });
+    }
+  });
+});

tests/cdpBrowserProvider.test.ts

@@ -109,6 +109,82 @@ describe("CdpBrowserProvider", () => {
     ).toBe(true);
   });
 
+  it("projects direct-session cancellation onto the requested operation", async () => {
+    const browser = await startFakeCdpBrowser({
+      pageScopedVersionWebSocket: true,
+      omitTargetWebSocket: true,
+    });
+    browsers.push(browser);
+    const controller = new AbortController();
+    const result = await new CdpBrowserProvider().observeSession(
+      observeWebSessionInputSchema.parse({
+        cdp_endpoint: browser.endpoint,
+        allowed_origins: [browser.allowedOrigin],
+        target_id: "allowed-page",
+        approved: true,
+        observation_ms: 1_000,
+      }),
+      {
+        signal: controller.signal,
+        progress: {
+          report(update) {
+            if (update.completed === 1) controller.abort();
+            return Promise.resolve();
+          },
+        },
+      },
+    );
+
+    expect(result).toMatchObject({
+      ok: false,
+      error: {
+        _tag: "AnalysisCancelledError",
+        operation: "observe_web_session",
+      },
+    });
+    const methods = browser.commands.map(({ method }) => method);
+    expect(methods).not.toContain("Target.attachToTarget");
+    expect(methods).not.toContain("Target.detachFromTarget");
+    expect(methods).not.toContain("Target.closeTarget");
+    expect(methods).not.toContain("Browser.close");
+  });
+
+  it("projects capture-window cancellation onto bundle analysis", async () => {
+    const browser = await startFakeCdpBrowser({
+      pageScopedVersionWebSocket: true,
+      omitTargetWebSocket: true,
+    });
+    browsers.push(browser);
+    const controller = new AbortController();
+    const result = await new CdpBrowserProvider().analyzeBundle(
+      analyzeWebBundleInputSchema.parse({
+        cdp_endpoint: browser.endpoint,
+        allowed_origins: [browser.allowedOrigin],
+        target_id: "allowed-page",
+        approved: true,
+        source_capture_approved: true,
+        observation_ms: 1_000,
+      }),
+      {
+        signal: controller.signal,
+        progress: {
+          report(update) {
+            if (update.completed === 2) controller.abort();
+            return Promise.resolve();
+          },
+        },
+      },
+    );
+
+    expect(result).toMatchObject({
+      ok: false,
+      error: {
+        _tag: "AnalysisCancelledError",
+        operation: "analyze_web_bundle",
+      },
+    });
+  });
+
   it("rejects empty browser attachment session identifiers", async () => {
     const browser = await startFakeCdpBrowser({ invalidAttachedSession: true });
     browsers.push(browser);
@@ -644,6 +720,58 @@ describe("CdpBrowserProvider", () => {
     );
   });
 
+  it("ends a browser session when its flat target session detaches", async () => {
+    const browser = await startFakeCdpBrowser({
+      sessionTimeline: "target_detached",
+    });
+    browsers.push(browser);
+    const result = await new CdpBrowserProvider().observeSession(
+      observeWebSessionInputSchema.parse({
+        cdp_endpoint: browser.endpoint,
+        allowed_origins: [browser.allowedOrigin],
+        target_id: "allowed-page",
+        approved: true,
+        observation_ms: 1_000,
+      }),
+    );
+
+    if (!result.ok) throw result.error;
+    expect(result.value.window.end_reason).toBe("target_terminated");
+    expect(result.value.timeline.at(-1)).toMatchObject({
+      type: "target_terminated",
+      detail: "target_terminated",
+    });
+  });
+
+  it("ends a direct page session when its transport disconnects", async () => {
+    const browser = await startFakeCdpBrowser({
+      pageScopedVersionWebSocket: true,
+      omitTargetWebSocket: true,
+      closeAfterMethod: "Page.setLifecycleEventsEnabled",
+    });
+    browsers.push(browser);
+    const result = await new CdpBrowserProvider().observeSession(
+      observeWebSessionInputSchema.parse({
+        cdp_endpoint: browser.endpoint,
+        allowed_origins: [browser.allowedOrigin],
+        target_id: "allowed-page",
+        approved: true,
+        observation_ms: 1_000,
+      }),
+    );
+
+    if (!result.ok) throw result.error;
+    expect(result.value.window.end_reason).toBe("target_terminated");
+    expect(result.value.timeline.at(-1)).toMatchObject({
+      type: "target_terminated",
+      detail: "target_terminated",
+    });
+    const methods = browser.commands.map(({ method }) => method);
+    expect(methods).not.toContain("Target.attachToTarget");
+    expect(methods).not.toContain("Target.detachFromTarget");
+    expect(methods).not.toContain("Target.closeTarget");
+  });
+
   it("discovers untrusted WebMCP declarations without registering or invoking them", async () => {
     const browser = await startFakeCdpBrowser({ webMcpTools: true });
     browsers.push(browser);
@@ -1198,7 +1326,10 @@ describe("CdpBrowserProvider", () => {
     const result = await pending;
     expect(result).toMatchObject({
       ok: false,
-      error: { _tag: "AnalysisCancelledError" },
+      error: {
+        _tag: "AnalysisCancelledError",
+        operation: "inspect_web_page",
+      },
     });
     const methods = browser.commands.map(({ method }) => method);
     expect(methods).toContain("Target.detachFromTarget");

tests/cdpConnection.test.ts

@@ -19,7 +19,10 @@ describe("CDP connection", () => {
   it("correlates concurrent command responses over a real WebSocket", async () => {
     const browser = await startFakeCdpBrowser();
     browsers.push(browser);
-    const connection = await CdpConnection.connect(browser.browserWebSocketUrl);
+    const connection = await CdpConnection.connect(
+      browser.browserWebSocketUrl,
+      "inspect_web_page",
+    );
     try {
       const [attached, frames] = await Promise.all([
         connection.send("Target.attachToTarget"),
@@ -37,13 +40,16 @@ describe("CDP connection", () => {
   it("returns a typed timeout for an unresponsive CDP command", async () => {
     const browser = await startFakeCdpBrowser({ hangOnMethod: "Page.enable" });
     browsers.push(browser);
-    const connection = await CdpConnection.connect(browser.browserWebSocketUrl);
+    const connection = await CdpConnection.connect(
+      browser.browserWebSocketUrl,
+      "observe_web_session",
+    );
     vi.useFakeTimers();
     try {
       const pending = connection.send("Page.enable");
       const assertion = expect(pending).rejects.toMatchObject({
         _tag: "AnalysisTimeoutError",
-        operation: "inspect_web_page",
+        operation: "observe_web_session",
         timeoutMs: 5_000,
       });
       await vi.advanceTimersByTimeAsync(5_000);

tests/cdpElectronProvider.test.ts

@@ -142,6 +142,28 @@ describe("CdpElectronProvider", () => {
     ).toBe(true);
   });
 
+  it("maps cancelled Electron discovery to the Electron operation", async () => {
+    const root = await electronFixture();
+    const controller = new AbortController();
+    controller.abort();
+    const result = await new CdpElectronProvider().listTargets(
+      listElectronTargetsInputSchema.parse({
+        cdp_endpoint: "http://127.0.0.1:9222",
+        allowed_file_roots: [root],
+        approved: true,
+      }),
+      { signal: controller.signal },
+    );
+
+    expect(result).toMatchObject({
+      ok: false,
+      error: {
+        _tag: "AnalysisCancelledError",
+        operation: "list_electron_targets",
+      },
+    });
+  });
+
   it("captures Electron script source only after separate approval", async () => {
     const root = await electronFixture();
     const browser = await startFakeCdpBrowser({

tests/cliPolicyCommands.test.ts

@@ -0,0 +1,95 @@
+import { execFile } from "node:child_process";
+import { mkdtemp, rm } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { promisify } from "node:util";
+
+import { afterEach, describe, expect, it } from "vitest";
+
+import {
+  readProjectPermissionStore,
+  writeProjectPermissionStore,
+} from "../src/application/ProjectPermissionStore.js";
+
+const execFileAsync = promisify(execFile);
+const CLI_INTEGRATION_TIMEOUT_MS = 60_000;
+const roots: string[] = [];
+
+afterEach(async () => {
+  await Promise.all(
+    roots.splice(0).map((root) => rm(root, { recursive: true, force: true })),
+  );
+});
+
+describe("policy CLI revocation", () => {
+  it(
+    "requires confirmation in structured mode and accepts explicit approval",
+    async () => {
+      const project = await mkdtemp(join(tmpdir(), "rea-policy-cli-"));
+      roots.push(project);
+      const store = join(project, ".rea", "permissions.json");
+      const grant = {
+        grant_id: "project:evidence-read",
+        capability: "evidence_read" as const,
+        roots: [project],
+        executables: [],
+        environment_names: [],
+        network: "none" as const,
+        mount: false,
+        lifetime: "project" as const,
+        operation_identity: null,
+        expires_at: null,
+      };
+      expect(
+        (await writeProjectPermissionStore(store, project, [grant])).ok,
+      ).toBe(true);
+      const environment = {
+        ...process.env,
+        REA_PERMISSION_PROJECT_ROOT: project,
+        REA_PERMISSION_PROJECT_STORE: store,
+      };
+
+      const unapproved = await execFileAsync(
+        process.execPath,
+        ["scripts/rea.mjs", "--json", "policy", "revoke", grant.grant_id],
+        { cwd: process.cwd(), env: environment },
+      ).catch((cause: unknown) => cause);
+      expect(unapproved).toMatchObject({ code: 1, stderr: "" });
+      expect(
+        JSON.parse((unapproved as { readonly stdout: string }).stdout),
+      ).toEqual({
+        error: "ConfirmationRequired",
+        message: "Policy grant revocation requires confirmation",
+        grant_id: grant.grant_id,
+        remediation:
+          "Verify the grant ID, then rerun the same command with --yes.",
+      });
+      expect(await readProjectPermissionStore(store, project)).toMatchObject({
+        ok: true,
+        value: { grants: [grant] },
+      });
+
+      const approved = await execFileAsync(
+        process.execPath,
+        [
+          "scripts/rea.mjs",
+          "--json",
+          "policy",
+          "revoke",
+          grant.grant_id,
+          "--yes",
+        ],
+        { cwd: process.cwd(), env: environment },
+      );
+      expect(JSON.parse(approved.stdout)).toEqual({
+        revoked: grant.grant_id,
+        reload: "Send SIGHUP to the REA MCP process",
+      });
+      expect(await readProjectPermissionStore(store, project)).toMatchObject({
+        ok: true,
+        value: { grants: [] },
+      });
+    },
+    CLI_INTEGRATION_TIMEOUT_MS,
+  );
+});

tests/fixtures/fakeCdpBrowser.ts

@@ -51,7 +51,11 @@ interface FakeOptions {
   readonly binaryWebSocketEvent?: boolean;
   readonly invalidBinaryWebSocketEvent?: boolean;
   readonly sourceMapBody?: string;
-  readonly sessionTimeline?: "same_origin" | "outside_policy";
+  readonly sessionTimeline?:
+    | "same_origin"
+    | "outside_policy"
+    | "target_detached";
+  readonly closeAfterMethod?: string;
   readonly sensitiveShapes?: boolean;
   readonly invalidResponseBodyBase64?: boolean;
   readonly webMcpTools?: boolean;
@@ -183,6 +187,8 @@ export const startFakeCdpBrowser = async (
       if (options.malformedEventShapeOnMethod === command.method)
         socket.send(JSON.stringify({ method: 42 }));
       emitEvents(socket, command, port, options);
+      if (options.closeAfterMethod === command.method)
+        setImmediate(() => socket.close());
     });
   });
   await new Promise<void>((resolve, reject) => {
@@ -963,6 +969,11 @@ const emitEvents = (
       name: "networkIdle",
       timestamp: 15,
     });
+    if (options.sessionTimeline === "target_detached")
+      event(socket, "Target.detachedFromTarget", undefined, {
+        sessionId: command.sessionId,
+        targetId: "allowed-page",
+      });
   }
 };
 

tests/fixtures/processFidelity.mjs

@@ -1,6 +1,12 @@
 import { spawn } from "node:child_process";
 
 const mode = process.argv[2];
+const treeRunMarker = process.argv[3];
+const treeRunArguments = (childMode) => [
+  process.argv[1],
+  childMode,
+  ...(treeRunMarker === undefined ? [] : [treeRunMarker]),
+];
 
 if (mode === "interactive") {
   process.stdin.setRawMode?.(true);
@@ -32,14 +38,14 @@ if (mode === "interactive") {
     process.exit(0);
   }, 25);
 } else if (mode === "tree-child") {
-  spawn(process.execPath, [process.argv[1], "tree-grandchild"], {
+  spawn(process.execPath, treeRunArguments("tree-grandchild"), {
     stdio: "ignore",
   });
   setInterval(() => undefined, 1_000);
 } else if (mode === "tree-grandchild") {
   setInterval(() => undefined, 1_000);
 } else if (mode === "tree") {
-  spawn(process.execPath, [process.argv[1], "tree-child"], { stdio: "ignore" });
+  spawn(process.execPath, treeRunArguments("tree-child"), { stdio: "ignore" });
   process.stdout.write("tree-ready\n");
   setInterval(() => undefined, 1_000);
 } else if (mode === "crash") {

tests/investigationMcp.test.ts

@@ -15,6 +15,7 @@ import {
   PROCESS_COMPARISON_EVIDENCE,
 } from "../src/contracts/investigationExamples.js";
 import { createEvidence, parseEvidence } from "../src/domain/evidence.js";
+import { changedBehaviorResultSchema } from "../src/domain/changedBehavior.js";
 import { jsonObjectSchema, jsonValueSchema } from "../src/domain/jsonValue.js";
 import { createServer } from "../src/server/createServer.js";
 import { observed } from "./fixtures/analysisExecution.js";
@@ -214,6 +215,85 @@ describe("investigation MCP workflows", () => {
     }
   });
 
+  it("replays a selected complete run after input access is removed", async () => {
+    const directory = await mkdtemp(
+      join(tmpdir(), "rea-investigation-replay-"),
+    );
+    const left = join(directory, "left");
+    const right = join(directory, "right");
+    const workspace = join(directory, "workspace.json");
+    await Promise.all([mkdir(left), mkdir(right)]);
+    await Promise.all([
+      writeFile(join(left, "feature.txt"), "old\n"),
+      writeFile(join(right, "feature.txt"), "new\n"),
+    ]);
+    const filePolicy = evidencePolicy(directory);
+    const investigationRun = {
+      approved: true,
+      workspace_path: workspace,
+      workspace_name: "selected-replay",
+      left_path: left,
+      right_path: right,
+      options: { page_size: 500, change_limit: 100 },
+    };
+    const writer = await investigationAuthority(directory, true);
+    const initial = await connected(filePolicy, [directory], writer);
+    let runId: string | undefined;
+    try {
+      const created = await initial.client.callTool({
+        name: "find_changed_behavior",
+        arguments: { investigation_run: investigationRun },
+      });
+      expect(created.isError, JSON.stringify(created)).not.toBe(true);
+      const evidence = parseEvidence(
+        z.object({ result: z.unknown() }).parse(created.structuredContent)
+          .result,
+      );
+      const result = changedBehaviorResultSchema.parse(
+        evidence.normalized_result,
+      );
+      if (result.investigation_run === undefined)
+        throw new Error("missing investigation run summary");
+      runId = result.investigation_run.run_id;
+    } finally {
+      await close(initial.session, initial.server, initial.client);
+    }
+    if (runId === undefined) throw new Error("missing completed run ID");
+
+    await Promise.all([
+      rm(left, { recursive: true, force: true }),
+      rm(right, { recursive: true, force: true }),
+    ]);
+    const workspaceOnly = await permissionAuthorityForRoot(
+      directory,
+      [
+        "investigation_workspace_read",
+        "investigation_workspace_write",
+        "investigation_input",
+      ],
+      ["investigation_workspace_read"],
+    );
+    const replay = await connected(filePolicy, [], workspaceOnly);
+    try {
+      const cached = await replay.client.callTool({
+        name: "find_changed_behavior",
+        arguments: {
+          investigation_run: {
+            ...investigationRun,
+            replay_run_id: runId,
+          },
+        },
+      });
+      expect(cached.isError, JSON.stringify(cached)).not.toBe(true);
+      expect(
+        await readInvestigationWorkspace(workspace, filePolicy),
+      ).toMatchObject({ ok: true, value: { revision: 3 } });
+    } finally {
+      await close(replay.session, replay.server, replay.client);
+      await rm(directory, { recursive: true, force: true });
+    }
+  });
+
   it("refuses automatic artifact reads outside operator-approved roots", async () => {
     const directory = await mkdtemp(join(tmpdir(), "rea-investigation-mcp-"));
     const approvedInputs = join(directory, "approved-inputs");

tests/investigationWorkspace.test.ts

@@ -12,7 +12,7 @@ import { createHash } from "node:crypto";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
 
-import { afterEach, describe, expect, it } from "vitest";
+import { afterEach, describe, expect, it, vi } from "vitest";
 import { createPackageWithOptions } from "@electron/asar";
 import canonicalize from "canonicalize";
 
@@ -21,16 +21,25 @@ import {
   readInvestigationWorkspace,
   writeInvestigationWorkspace,
 } from "../src/application/InvestigationWorkspaceStore.js";
-import { changedBehaviorResultSchema } from "../src/domain/changedBehavior.js";
+import { compareArtifacts } from "../src/domain/artifactComparison.js";
+import { artifactInventoryResultSchema } from "../src/domain/artifactGraph.js";
+import {
+  changedBehaviorResultSchema,
+  findChangedBehavior,
+} from "../src/domain/changedBehavior.js";
+import { createEvidence, type Evidence } from "../src/domain/evidence.js";
 import { createEvidenceBundle } from "../src/domain/evidenceBundle.js";
 import type { EvidenceFilePolicy } from "../src/domain/evidenceBundle.js";
 import {
   createInvestigationWorkspace,
   crossVersionInvestigationInputSchema,
   investigationRunSchema,
+  investigationRunSummarySchema,
   parseInvestigationWorkspace,
   serializeInvestigationWorkspace,
 } from "../src/domain/investigationWorkspace.js";
+import type { JsonValue } from "../src/domain/jsonValue.js";
+import { ok } from "../src/domain/result.js";
 
 const digestCanonical = (value: unknown): string => {
   const encoded = canonicalize(value);
@@ -54,6 +63,41 @@ const policy = (root: string): EvidenceFilePolicy => ({
   maxNodes: 1_000_000,
 });
 
+const recreateEvidence = (
+  evidence: Evidence,
+  overrides: {
+    readonly parameters?: Readonly<Record<string, JsonValue>>;
+    readonly result?: JsonValue;
+    readonly evidenceLinks?: readonly string[];
+  },
+): Evidence =>
+  createEvidence(
+    evidence.subject === null
+      ? undefined
+      : {
+          path: evidence.subject.local_path,
+          sha256: evidence.subject.digest.sha256,
+          format: evidence.subject.format,
+          ...(evidence.subject.architecture === null
+            ? {}
+            : { architecture: evidence.subject.architecture }),
+        },
+    evidence.provider,
+    {
+      predicateType: evidence.predicate_type,
+      operation: evidence.operation,
+      parameters: overrides.parameters ?? evidence.parameters,
+      result: overrides.result ?? evidence.normalized_result,
+      rawResult: evidence.raw_result,
+      confidence: evidence.confidence,
+      authority: evidence.authority,
+      environment: evidence.environment,
+      limitations: evidence.limitations,
+      locations: evidence.locations,
+      evidenceLinks: overrides.evidenceLinks ?? evidence.evidence_links,
+    },
+  );
+
 const fixture = async () => {
   directory = await mkdtemp(join(tmpdir(), "rea-workspace-"));
   const left = join(directory, "left");
@@ -239,6 +283,235 @@ describe("persistent cross-version investigation workspace", () => {
     });
   });
 
+  it("replays an explicitly selected complete run without input access", async () => {
+    const { left, right, input } = await fixture();
+    if (directory === undefined) throw new Error("missing fixture root");
+    const completed = await runCrossVersionInvestigation(
+      input,
+      policy(directory),
+      { inputRoots: [directory] },
+    );
+    if (!completed.ok) throw completed.error;
+    const run = completed.value.workspace.runs[0];
+    if (run === undefined) throw new Error("missing completed run");
+    await Promise.all([
+      rm(left, { recursive: true, force: true }),
+      rm(right, { recursive: true, force: true }),
+    ]);
+    const authorizeInputRead = vi.fn(() => Promise.resolve(ok(null)));
+
+    await expect(
+      runCrossVersionInvestigation(
+        { ...input, replay_run_id: run.run_id },
+        policy(directory),
+        { inputRoots: [], authorizeInputRead },
+      ),
+    ).resolves.toMatchObject({
+      ok: true,
+      value: {
+        reused: true,
+        evidence: { evidence_id: completed.value.evidence.evidence_id },
+      },
+    });
+    expect(authorizeInputRead).not.toHaveBeenCalled();
+
+    for (const replayInput of [
+      { ...input, replay_run_id: `run_${"f".repeat(64)}` },
+      { ...input, right_path: `${right}-other`, replay_run_id: run.run_id },
+    ])
+      await expect(
+        runCrossVersionInvestigation(replayInput, policy(directory), {
+          inputRoots: [],
+          authorizeInputRead,
+        }),
+      ).resolves.toMatchObject({
+        ok: false,
+        error: {
+          _tag: "InvestigationWorkspaceError",
+          reason: "revision-conflict",
+        },
+      });
+    expect(authorizeInputRead).not.toHaveBeenCalled();
+
+    const byId = new Map(
+      completed.value.workspace.bundle.records.map((record) => [
+        record.evidence_id,
+        record,
+      ]),
+    );
+    const evidenceFor = (ids: readonly string[]): Evidence[] =>
+      ids.map((id) => {
+        const evidence = byId.get(id);
+        if (evidence === undefined)
+          throw new Error("missing inventory fixture Evidence");
+        return evidence;
+      });
+    const leftPages = evidenceFor(run.left_inventory_evidence_ids);
+    const rightPages = evidenceFor(run.right_inventory_evidence_ids);
+    const comparison = byId.get(run.comparison_evidence_id ?? "");
+    const result = byId.get(run.result_evidence_id ?? "");
+    if (comparison === undefined || result === undefined)
+      throw new Error("missing completed fixture Evidence");
+    const forgeWorkspace = (forgedLeftPages: readonly Evidence[]) => {
+      const comparisonResult = compareArtifacts(
+        forgedLeftPages,
+        rightPages,
+        0,
+        run.options.change_limit,
+      );
+      const forgedComparison = recreateEvidence(comparison, {
+        parameters: {
+          left_evidence_ids: forgedLeftPages.map(({ evidence_id: id }) => id),
+          right_evidence_ids: rightPages.map(({ evidence_id: id }) => id),
+          offset: 0,
+          limit: run.options.change_limit,
+        },
+        result: comparisonResult,
+        evidenceLinks: [
+          ...forgedLeftPages.map(({ evidence_id: id }) => id),
+          ...rightPages.map(({ evidence_id: id }) => id),
+        ],
+      });
+      const resultLimit = Math.min(run.options.change_limit, 100);
+      const changed = findChangedBehavior([forgedComparison], 0, resultLimit);
+      const summary = investigationRunSummarySchema.parse({
+        schema_version: 1,
+        workspace_id: completed.value.workspace.workspace_id,
+        run_id: run.run_id,
+        left_manifest_id: run.left.manifest_id,
+        right_manifest_id: run.right.manifest_id,
+        inventory_evidence_count: forgedLeftPages.length + rightPages.length,
+        comparison_evidence_id: forgedComparison.evidence_id,
+        limitations: run.limitations,
+      });
+      const forgedResult = recreateEvidence(result, {
+        parameters: {
+          workspace_id: completed.value.workspace.workspace_id,
+          run_id: run.run_id,
+          comparison_evidence_ids: [forgedComparison.evidence_id],
+          offset: 0,
+          limit: resultLimit,
+        },
+        result: { ...changed, investigation_run: summary },
+        evidenceLinks: changed.evidence_links,
+      });
+      const forgedRun = investigationRunSchema.parse({
+        ...run,
+        left_inventory_evidence_ids: forgedLeftPages.map(
+          ({ evidence_id: id }) => id,
+        ),
+        comparison_evidence_id: forgedComparison.evidence_id,
+        result_evidence_id: forgedResult.evidence_id,
+      });
+      const records = new Map(
+        [
+          ...completed.value.workspace.bundle.records,
+          ...forgedLeftPages,
+          forgedComparison,
+          forgedResult,
+        ].map((record) => [record.evidence_id, record]),
+      );
+      return createInvestigationWorkspace(
+        input.workspace_name,
+        createEvidenceBundle([...records.values()]),
+        [forgedRun],
+      );
+    };
+    const firstPage = leftPages[0]!;
+    const firstPageResult = artifactInventoryResultSchema.parse(
+      firstPage.normalized_result,
+    );
+    const extraOffset = leftPages.length * input.options.page_size;
+    const extraPage = recreateEvidence(firstPage, {
+      parameters: {
+        ...firstPage.parameters,
+        node_offset: extraOffset,
+        occurrence_offset: extraOffset,
+        edge_offset: extraOffset,
+      },
+      result: {
+        ...firstPageResult,
+        nodes: {
+          ...firstPageResult.nodes,
+          items: [],
+          offset: extraOffset,
+          next_offset: null,
+        },
+        occurrences: {
+          ...firstPageResult.occurrences,
+          items: [],
+          offset: extraOffset,
+          next_offset: null,
+        },
+        edges: {
+          ...firstPageResult.edges,
+          items: [],
+          offset: extraOffset,
+          next_offset: null,
+        },
+      },
+    });
+    const forgedVariants = [
+      {
+        name: "controls",
+        pages: [
+          recreateEvidence(firstPage, {
+            parameters: {
+              ...firstPage.parameters,
+              max_entries: input.options.max_entries - 1,
+            },
+          }),
+          ...leftPages.slice(1),
+        ],
+      },
+      {
+        name: "page-total",
+        pages: [
+          recreateEvidence(firstPage, {
+            result: {
+              ...firstPageResult,
+              nodes: {
+                ...firstPageResult.nodes,
+                total: firstPageResult.nodes.total + 1,
+              },
+            },
+          }),
+          ...leftPages.slice(1),
+        ],
+      },
+      { name: "page-count", pages: [...leftPages, extraPage] },
+    ] as const;
+    for (const variant of forgedVariants) {
+      const forgedPath = join(directory, `forged-${variant.name}.json`);
+      expect(
+        await writeInvestigationWorkspace(
+          forgeWorkspace(variant.pages),
+          forgedPath,
+          null,
+          policy(directory),
+        ),
+      ).toMatchObject({ ok: true });
+      await expect(
+        runCrossVersionInvestigation(
+          {
+            ...input,
+            workspace_path: forgedPath,
+            replay_run_id: run.run_id,
+          },
+          policy(directory),
+          { inputRoots: [], authorizeInputRead },
+        ),
+      ).resolves.toMatchObject({
+        ok: false,
+        error: {
+          _tag: "InvestigationWorkspaceError",
+          reason: "revision-conflict",
+        },
+      });
+    }
+    expect(authorizeInputRead).not.toHaveBeenCalled();
+  });
+
   it("enforces shared JSON depth limits while reading workspaces", async () => {
     const { path, input } = await fixture();
     if (directory === undefined) throw new Error("missing fixture root");
@@ -300,6 +573,26 @@ describe("persistent cross-version investigation workspace", () => {
       ),
     ).toMatchObject({ ok: true });
 
+    const authorizeInputRead = vi.fn(() => Promise.resolve(ok(null)));
+    await expect(
+      runCrossVersionInvestigation(
+        {
+          ...input,
+          workspace_path: resumePath,
+          replay_run_id: partialRun.run_id,
+        },
+        policy(directory),
+        { inputRoots: [], authorizeInputRead },
+      ),
+    ).resolves.toMatchObject({
+      ok: false,
+      error: {
+        _tag: "InvestigationWorkspaceError",
+        reason: "revision-conflict",
+      },
+    });
+    expect(authorizeInputRead).not.toHaveBeenCalled();
+
     const resumed = await runCrossVersionInvestigation(
       { ...input, workspace_path: resumePath },
       policy(directory),

tests/mainErrors.test.ts

@@ -18,7 +18,13 @@ const dependencies = (
   serve,
   writeStderr: (text) => output.push(text),
   setExitCode: (code) => exitCodes.push(code),
-  registerShutdown: (handler) => shutdown.push(handler),
+  registerShutdown: (handler) => {
+    shutdown.push(handler);
+    return () => {
+      const index = shutdown.indexOf(handler);
+      if (index >= 0) shutdown.splice(index, 1);
+    };
+  },
 });
 
 describe("MCP runtime errors", () => {
@@ -52,6 +58,7 @@ describe("MCP runtime errors", () => {
     shutdown[0]?.();
     await nextTurn();
     expect(closeCalls).toBe(1);
+    expect(shutdown).toEqual([]);
   });
 
   it("reports transport startup failure without its cause", async () => {
@@ -87,6 +94,7 @@ describe("MCP runtime errors", () => {
     );
     shutdown[0]?.();
     await nextTurn();
+    expect(shutdown).toEqual([]);
     expect(exitCodes).toEqual([1]);
     expect(output).toEqual([
       "REA could not close cleanly. End the REA process before starting it again.\n",

tests/processCapture.test.ts

@@ -1,3 +1,4 @@
+import { randomUUID } from "node:crypto";
 import { mkdtemp, readFile, rm, symlink, writeFile } from "node:fs/promises";
 import { tmpdir } from "node:os";
 import { dirname, join } from "node:path";
@@ -19,7 +20,10 @@ import {
 } from "../src/application/ProcessCaptureLifecycle.js";
 import { ProcessCheckpoints } from "../src/application/ProcessCheckpoints.js";
 import { normalizeProcessSamples } from "../src/application/ProcessNormalization.js";
-import { readLinuxChildren } from "../src/application/ProcessSampling.js";
+import {
+  isInitializedPtyRoot,
+  readLinuxChildren,
+} from "../src/application/ProcessSampling.js";
 import { TerminalRenderer } from "../src/application/TerminalRenderer.js";
 import {
   authorizeProcessScenario,
@@ -37,6 +41,7 @@ const processFixture = fileURLToPath(
   new URL("./fixtures/processFidelity.mjs", import.meta.url),
 );
 const execFileAsync = promisify(execFile);
+const PROCESS_CAPTURE_INTEGRATION_TIMEOUT_MS = 20_000;
 
 const emptyCapture = (): ProcessCapture => {
   const normalization = {
@@ -211,6 +216,43 @@ describe("process capture domain", () => {
     ).toEqual([201, 202, 203]);
   });
 
+  it("admits PTY samples only after stable session and token setup", () => {
+    const initialized = {
+      pid: 100,
+      parent_pid: 10,
+      process_group_id: 100,
+      session_id: 100,
+      startTime: "200",
+    };
+    expect(
+      isInitializedPtyRoot({
+        rootPid: 100,
+        expectedRunId: "run-token",
+        before: { ...initialized, process_group_id: 10, session_id: 10 },
+        observedRunId: undefined,
+        after: initialized,
+      }),
+    ).toBe(false);
+    expect(
+      isInitializedPtyRoot({
+        rootPid: 100,
+        expectedRunId: "run-token",
+        before: initialized,
+        observedRunId: "run-token",
+        after: { ...initialized, startTime: "201" },
+      }),
+    ).toBe(false);
+    expect(
+      isInitializedPtyRoot({
+        rootPid: 100,
+        expectedRunId: "run-token",
+        before: initialized,
+        observedRunId: "run-token",
+        after: initialized,
+      }),
+    ).toBe(true);
+  });
+
   it("keeps interaction and shim residual uncertainty in separate scopes", () => {
     const baseCapture = emptyCapture();
     const interaction = parseProcessCapture({
@@ -839,95 +881,103 @@ describe("process capture adapter", () => {
     }
   });
 
-  it("renders terminal state, records shim invocations, and captures literal checkpoints", async () => {
-    const root = await mkdtemp(join(tmpdir(), "rea-v3-test-"));
-    const script = join(root, "scenario.mjs");
-    await writeFile(
-      script,
-      [
-        'import { spawnSync } from "node:child_process";',
-        'const result = spawnSync("codex", ["--version"], { encoding: "utf8" });',
-        'const node = spawnSync("node", ["--version"], { encoding: "utf8" });',
-        "process.stdout.write(`probe:${result.stdout}`);",
-        "process.stdout.write(`runtime:${node.stdout}`);",
-      ].join("\n"),
-    );
-    try {
-      const capability = await probeProcessCaptureCapability();
-      if (!capability.available) return;
-      const result = await captureProcessScenario(
-        parseProcessScenario({
-          approved: true,
-          executable: process.execPath,
-          arguments: [script],
-          working_directory: root,
-          filesystem_roots: [root],
-          checkpoints: [
-            {
-              name: "probe_seen",
-              trigger: { type: "terminal_literal", value: "probe:codex 1.2.3" },
-            },
-          ],
-          command_shims: [
-            {
-              name: "codex",
-              routes: [
-                {
-                  arguments: ["--version"],
-                  outputs: [
-                    { at_ms: 0, stream: "stdout", data: "codex 1.2.3\n" },
-                  ],
-                  termination: { type: "exit", code: 0 },
-                },
-              ],
-            },
-            {
-              name: "node",
-              routes: [
-                {
-                  arguments: ["--version"],
-                  outputs: [
-                    { at_ms: 0, stream: "stdout", data: "node 9.8.7\n" },
-                  ],
-                  termination: { type: "exit", code: 0 },
-                },
-              ],
-            },
-          ],
-        }),
-        {
-          enabled: true,
-          executableRoots: [dirname(process.execPath)],
-          workingRoots: [root],
-          allowedEnvironment: [],
-          allowExternalNetwork: true,
-        },
+  it(
+    "renders terminal state, records shim invocations, and captures literal checkpoints",
+    async () => {
+      const root = await mkdtemp(join(tmpdir(), "rea-v3-test-"));
+      const script = join(root, "scenario.mjs");
+      await writeFile(
+        script,
+        [
+          'import { spawnSync } from "node:child_process";',
+          'const result = spawnSync("codex", ["--version"], { encoding: "utf8" });',
+          'const node = spawnSync("node", ["--version"], { encoding: "utf8" });',
+          "process.stdout.write(`probe:${result.stdout}`);",
+          "process.stdout.write(`runtime:${node.stdout}`);",
+        ].join("\n"),
       );
-      expect(result.ok).toBe(true);
-      if (!result.ok) throw result.error;
-      expect(result.value.schema_version).toBe(4);
-      expect(result.value.rendered_frames.at(-1)?.lines.join("\n")).toContain(
-        "probe:codex 1.2.3",
-      );
-      expect(result.value.shim_events).toEqual([
-        expect.objectContaining({
-          command: "codex",
-          arguments: ["--version"],
-          outcome: "matched",
-        }),
-        expect.objectContaining({
-          command: "node",
-          arguments: ["--version"],
-          outcome: "matched",
-        }),
-      ]);
-      expect(
-        result.value.filesystem_checkpoints.map(({ name }) => name),
-      ).toEqual(["before", "probe_seen", "after_settlement"]);
-    } finally {
-      await rm(root, { recursive: true, force: true });
-    }
-  });
+      try {
+        const capability = await probeProcessCaptureCapability();
+        if (!capability.available) return;
+        const result = await captureProcessScenario(
+          parseProcessScenario({
+            approved: true,
+            executable: process.execPath,
+            arguments: [script],
+            working_directory: root,
+            filesystem_roots: [root],
+            checkpoints: [
+              {
+                name: "probe_seen",
+                trigger: {
+                  type: "terminal_literal",
+                  value: "probe:codex 1.2.3",
+                },
+              },
+            ],
+            command_shims: [
+              {
+                name: "codex",
+                routes: [
+                  {
+                    arguments: ["--version"],
+                    outputs: [
+                      { at_ms: 0, stream: "stdout", data: "codex 1.2.3\n" },
+                    ],
+                    termination: { type: "exit", code: 0 },
+                  },
+                ],
+              },
+              {
+                name: "node",
+                routes: [
+                  {
+                    arguments: ["--version"],
+                    outputs: [
+                      { at_ms: 0, stream: "stdout", data: "node 9.8.7\n" },
+                    ],
+                    termination: { type: "exit", code: 0 },
+                  },
+                ],
+              },
+            ],
+            timeout_ms: 5_000,
+            idle_timeout_ms: 5_000,
+          }),
+          {
+            enabled: true,
+            executableRoots: [dirname(process.execPath)],
+            workingRoots: [root],
+            allowedEnvironment: [],
+            allowExternalNetwork: true,
+          },
+        );
+        if (!result.ok) throw result.error;
+        expect(result.value.schema_version).toBe(4);
+        expect(result.value.rendered_frames.at(-1)?.lines.join("\n")).toContain(
+          "probe:codex 1.2.3",
+        );
+        expect(result.value.shim_events).toEqual([
+          expect.objectContaining({
+            command: "codex",
+            arguments: ["--version"],
+            outcome: "matched",
+          }),
+          expect.objectContaining({
+            command: "node",
+            arguments: ["--version"],
+            outcome: "matched",
+          }),
+        ]);
+        expect(
+          result.value.filesystem_checkpoints.map(({ name }) => name),
+        ).toEqual(["before", "probe_seen", "after_settlement"]);
+      } finally {
+        await rm(root, { recursive: true, force: true });
+      }
+    },
+    PROCESS_CAPTURE_INTEGRATION_TIMEOUT_MS,
+  );
 
   it("does not follow or disclose symlink targets outside declared roots", async () => {
     const root = await mkdtemp(join(tmpdir(), "rea-symlink-test-"));
@@ -1108,40 +1158,48 @@ describe("process capture adapter", () => {
     ]);
   });
 
-  it("samples and cleans a source-owned child and grandchild process tree", async () => {
-    const capability = await probeProcessCaptureCapability();
-    if (!capability.available) return;
-    const result = await captureProcessScenario(
-      parseProcessScenario({
-        approved: true,
-        executable: process.execPath,
-        arguments: [processFixture, "tree"],
-        working_directory: dirname(processFixture),
-        timeout_ms: 2_000,
-        idle_timeout_ms: 2_000,
-      }),
-      {
-        enabled: true,
-        executableRoots: [dirname(process.execPath)],
-        workingRoots: [dirname(processFixture)],
-        allowedEnvironment: [],
-        allowExternalNetwork: true,
-      },
-    );
-    expect(result.ok).toBe(true);
-    if (!result.ok) throw result.error;
-    const commands = result.value.process_samples.map(({ command }) => command);
-    expect(commands.some((command) => command.includes("tree-child"))).toBe(
-      true,
-    );
-    expect(
-      commands.some((command) => command.includes("tree-grandchild")),
-    ).toBe(true);
-    expect(JSON.stringify(result.value.process_samples)).not.toContain(
-      dirname(processFixture),
-    );
-    const { stdout } = await execFileAsync("ps", ["-axo", "command="]);
-    expect(stdout).not.toContain(`${processFixture} tree-child`);
-    expect(stdout).not.toContain(`${processFixture} tree-grandchild`);
-  });
+  it(
+    "samples and cleans a source-owned child and grandchild process tree",
+    async () => {
+      const capability = await probeProcessCaptureCapability();
+      if (!capability.available) return;
+      const runMarker = `rea-tree-${randomUUID()}`;
+      const result = await captureProcessScenario(
+        parseProcessScenario({
+          approved: true,
+          executable: process.execPath,
+          arguments: [processFixture, "tree", runMarker],
+          working_directory: dirname(processFixture),
+          timeout_ms: 5_000,
+          idle_timeout_ms: 5_000,
+        }),
+        {
+          enabled: true,
+          executableRoots: [dirname(process.execPath)],
+          workingRoots: [dirname(processFixture)],
+          allowedEnvironment: [],
+          allowExternalNetwork: true,
+        },
+      );
+      if (!result.ok) throw result.error;
+      const commands = result.value.process_samples.map(
+        ({ command }) => command,
+      );
+      expect(commands.some((command) => command.includes("tree-child"))).toBe(
+        true,
+      );
+      expect(commands.some((command) => command.includes("forks.js"))).toBe(
+        false,
+      );
+      expect(
+        commands.some((command) => command.includes("tree-grandchild")),
+      ).toBe(true);
+      expect(JSON.stringify(result.value.process_samples)).not.toContain(
+        dirname(processFixture),
+      );
+      const { stdout } = await execFileAsync("ps", ["-axo", "command="]);
+      expect(stdout).not.toContain(runMarker);
+    },
+    PROCESS_CAPTURE_INTEGRATION_TIMEOUT_MS,
+  );
 });

tests/processOwnership.test.ts

@@ -1,6 +1,7 @@
 import { describe, expect, it, vi } from "vitest";
 import {
   cleanupOwnedProcessGroup,
+  observeOwnedProcessGroup,
   parseProcessEnvironment,
   type ProcessOwnershipHost,
 } from "../src/application/ProcessOwnership.js";
@@ -26,6 +27,7 @@ const host = (
             pid: Number(pid),
             parentPid: Number(pid) === 100 ? 1 : 100,
             processGroupId: 100,
+            state: "S",
             command: "fixture",
           })),
         ),
@@ -63,10 +65,108 @@ describe("owned process-group cleanup", () => {
     expect(await cleanupOwnedProcessGroup(ownership, adapter)).toEqual({
       cleaned: false,
       reason: "process group contains an unowned or PID-reused process",
+      failures: [{ pid: 101, reason: "run-token-mismatch" }],
     });
     expect(signalGroup).not.toHaveBeenCalled();
   });
 
+  it("checks every member and aggregates ownership read failures", async () => {
+    const environment = vi.fn((pid: number) => {
+      if (pid === 100)
+        return Promise.reject(new Error("transient procfs read"));
+      return Promise.resolve(
+        pid === 101
+          ? { REA_PROCESS_RUN_ID: "different-run" }
+          : { REA_PROCESS_RUN_ID: "run-token" },
+      );
+    });
+    const signalGroup = vi.fn();
+    const adapter: ProcessOwnershipHost = {
+      listMembers: () =>
+        Promise.resolve(
+          [100, 101, 102].map((pid) => ({
+            pid,
+            parentPid: pid === 100 ? 1 : 100,
+            processGroupId: 100,
+            state: "S",
+            command: "fixture",
+          })),
+        ),
+      environment,
+      signalGroup,
+    };
+
+    expect(await cleanupOwnedProcessGroup(ownership, adapter)).toEqual({
+      cleaned: false,
+      reason: "process group contains an unowned or PID-reused process",
+      failures: [
+        { pid: 100, reason: "environment-unreadable" },
+        { pid: 101, reason: "run-token-mismatch" },
+      ],
+    });
+    expect(environment.mock.calls.map(([pid]) => pid)).toEqual([100, 101, 102]);
+    expect(signalGroup).not.toHaveBeenCalled();
+  });
+
+  it("ignores exited zombie members during live ownership checks", async () => {
+    const environment = vi.fn((pid: number) =>
+      Promise.resolve(pid === 101 ? {} : { REA_PROCESS_RUN_ID: "run-token" }),
+    );
+    const signalGroup = vi.fn();
+    const adapter: ProcessOwnershipHost = {
+      listMembers: () =>
+        Promise.resolve([
+          {
+            pid: 100,
+            parentPid: 1,
+            processGroupId: 100,
+            state: "S",
+            command: "fixture",
+          },
+          {
+            pid: 101,
+            parentPid: 100,
+            processGroupId: 100,
+            state: "Z",
+            command: "[node] <defunct>",
+          },
+        ]),
+      environment,
+      signalGroup,
+    };
+
+    expect(await cleanupOwnedProcessGroup(ownership, adapter)).toEqual({
+      cleaned: true,
+      signaled: true,
+    });
+    expect(environment).toHaveBeenCalledTimes(1);
+    expect(environment).toHaveBeenCalledWith(100);
+    expect(signalGroup).toHaveBeenCalledWith(100, "SIGKILL");
+  });
+
+  it("observes a zombie-only group as settled", async () => {
+    const environment = vi.fn(() => Promise.resolve({}));
+    const adapter: ProcessOwnershipHost = {
+      listMembers: () =>
+        Promise.resolve([
+          {
+            pid: 101,
+            parentPid: 1,
+            processGroupId: 100,
+            state: "Z+",
+            command: "[node] <defunct>",
+          },
+        ]),
+      environment,
+      signalGroup: vi.fn(),
+    };
+
+    expect(await observeOwnedProcessGroup(ownership, adapter)).toEqual({
+      state: "empty",
+    });
+    expect(environment).not.toHaveBeenCalled();
+  });
+
   it("is idempotent when the owned group has already exited", async () => {
     const { adapter } = host({});
     expect(await cleanupOwnedProcessGroup(ownership, adapter)).toEqual({

tests/referenceSourceGraph.test.ts

@@ -192,6 +192,23 @@ describe("historical source graph", () => {
       ).toThrow(/Complete inventory/u);
   });
 
+  it("keeps distinct failure reasons for the same path and parser", () => {
+    const partial = graphInput();
+    partial.inventory_state = "partial";
+    partial.parse_failures = [
+      { path: "src/main.ts", parser: "babel", reason: "First failure" },
+      { path: "src/main.ts", parser: "babel", reason: "Second failure" },
+    ];
+
+    expect(createHistoricalSourceGraph(partial).parse_failures).toEqual(
+      partial.parse_failures,
+    );
+    partial.parse_failures.push(partial.parse_failures[1]!);
+    expect(() => createHistoricalSourceGraph(partial)).toThrow(
+      /parse_failures.*unique/iu,
+    );
+  });
+
   it("rejects strict unknown fields, invalid VCS, dangling internal edges, and false manifests", () => {
     expect(() =>
       createHistoricalSourceGraph({ ...graphInput(), surprise: true }),

tests/runtime.test.ts

@@ -37,7 +37,7 @@ describe("production stdio runtime", () => {
         name: "current_document",
         arguments: {},
       });
-      expect(result.isError).not.toBe(true);
+      expect(result.isError === true).toBe(process.platform === "linux");
     } finally {
       await client.close();
       await transport.close();
@@ -53,7 +53,7 @@ describe("production stdio runtime", () => {
         mode: "mcp",
         layer: "server",
         tool: "current_document",
-        status: "ok",
+        status: process.platform === "linux" ? "error" : "ok",
       }),
     );
     expect(stderr).not.toContain("HOPPER_LOADER_ARGS_JSON");

tests/setup.test.ts

@@ -19,9 +19,11 @@ class FakeSetupHost implements SetupHost {
   hopper: string | undefined;
   hopperInstallSucceeds = true;
   skill: "installed" | "unchanged" | "failed" = "installed";
+  skillNeedsInstallation = true;
   clients: readonly SetupClient[] = [];
   clientResults = new Map<string, ClientConfigurationResult>();
   hopperInstalls = 0;
+  skillInstallations = 0;
   configurations = 0;
   doctorHealthy: boolean | undefined;
   linuxDemoRuntimeMissing = false;
@@ -62,8 +64,12 @@ class FakeSetupHost implements SetupHost {
       this.clientResults.get(client.name) ?? { status: "configured" },
     );
   };
-  installSkill = (): Promise<"installed" | "unchanged" | "failed"> =>
-    Promise.resolve(this.skill);
+  skillInstallationNeeded = (): Promise<boolean> =>
+    Promise.resolve(this.skillNeedsInstallation);
+  installSkill = (): Promise<"installed" | "unchanged" | "failed"> => {
+    this.skillInstallations += 1;
+    return Promise.resolve(this.skill);
+  };
   doctor = (): Promise<{
     healthy: boolean;
     hopperPath?: string;
@@ -126,6 +132,21 @@ describe("setup workflow", () => {
     );
   });
 
+  it("omits an aligned skill from the plan and does not reinstall it", async () => {
+    const host = new FakeSetupHost();
+    host.hopper = "/Applications/Hopper";
+    host.skillNeedsInstallation = false;
+
+    const result = await runSetup(options(true), host);
+
+    expect(result.status).toBe("ready");
+    expect(result.plannedActions.map(({ kind }) => kind)).not.toContain(
+      "install_skill",
+    );
+    expect(result.appliedActions).toEqual([]);
+    expect(host.skillInstallations).toBe(0);
+  });
+
   it("reports ready after an accepted Linux plan installs healthy Hopper", async () => {
     const host = new FakeSetupHost("linux");
     host.distribution = {
@@ -218,6 +239,19 @@ describe("setup workflow", () => {
     expect(host.hopperInstalls).toBe(0);
   });
 
+  it("treats --install-hopper as approval, not a healthy reinstall request", async () => {
+    const host = new FakeSetupHost();
+    host.hopper = "/Applications/Hopper";
+
+    const result = await runSetup(options(true, true), host);
+
+    expect(result.status).toBe("ready");
+    expect(result.plannedActions.map(({ kind }) => kind)).not.toContain(
+      "install_hopper",
+    );
+    expect(host.hopperInstalls).toBe(0);
+  });
+
   it("installs missing Linux demo dependencies for existing Hopper", async () => {
     const host = new FakeSetupHost("linux");
     host.distribution = {
@@ -297,6 +331,34 @@ describe("setup workflow", () => {
     expect(result.remediation).not.toContain("internal_client_key");
   });
 
+  it("records later client outcomes after an earlier configuration fails", async () => {
+    const host = new FakeSetupHost();
+    host.hopper = "/Applications/Hopper";
+    host.clients = [
+      { name: "before", configPath: "/before.json" },
+      { name: "broken", configPath: "/broken.json" },
+      { name: "after", configPath: "/after.json" },
+    ];
+    host.clientResults.set("broken", { status: "failed", reason: "write" });
+
+    const result = await runSetup(options(true), host);
+
+    expect(result.status).toBe("needs_human");
+    expect(host.configurations).toBe(3);
+    expect(result.clients).toEqual({
+      before: { status: "configured" },
+      broken: { status: "failed", reason: "write" },
+      after: { status: "configured" },
+    });
+    expect(result.appliedActions).toEqual([
+      "configured_before",
+      "configured_after",
+    ]);
+    expect(result.remediation).toBe(
+      "Agent configuration could not be updated. Check file permissions, then rerun setup.",
+    );
+  });
+
   it("explains skill installation recovery", async () => {
     const host = new FakeSetupHost();
     host.hopper = "/Applications/Hopper";

tests/setupSkill.test.ts

@@ -3,6 +3,7 @@ import { tmpdir } from "node:os";
 import { dirname, join } from "node:path";
 import { afterEach, describe, expect, it } from "vitest";
 import { installCanonicalSkill } from "../src/application/Setup.js";
+import { canonicalSkillInstallationNeeded } from "../src/application/SetupSkill.js";
 import { TOOL_CONTRACTS } from "../src/contracts/toolContracts.js";
 
 const roots: string[] = [];
@@ -32,6 +33,18 @@ describe("canonical skill transaction", () => {
       `tool_count: ${String(TOOL_CONTRACTS.length)}`,
     );
     expect(await readFile(sibling, "utf8")).toBe("unrelated skill\n");
+    expect(await canonicalSkillInstallationNeeded(home)).toBe(false);
     expect(await installCanonicalSkill(home)).toBe("unchanged");
   });
+
+  it("reports a missing or stale canonical skill as needing installation", async () => {
+    const home = await mkdtemp(join(tmpdir(), "rea-skill-plan-test-"));
+    roots.push(home);
+    const destination = join(home, ".agents/skills/rea-analysis/SKILL.md");
+
+    expect(await canonicalSkillInstallationNeeded(home)).toBe(true);
+    await mkdir(dirname(destination), { recursive: true });
+    await writeFile(destination, "stale managed skill\n");
+    expect(await canonicalSkillInstallationNeeded(home)).toBe(true);
+  });
 });

vitest.config.ts

@@ -1,3 +1,6 @@
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+
 import { defineConfig } from "vitest/config";
 
 export default defineConfig({
@@ -8,6 +11,10 @@ export default defineConfig({
     coverage: {
       enabled: true,
       provider: "v8",
+      reportsDirectory: join(
+        tmpdir(),
+        `rea-vitest-coverage-${String(process.pid)}`,
+      ),
       include: ["src/**"],
       thresholds: {
         statements: 65,