diff --git a/ARCHITECTURE.md b/ARCHITECTURE.md
index 9bc6b43..49bc6cc 100644
--- a/ARCHITECTURE.md
+++ b/ARCHITECTURE.md
@@ -22,6 +22,8 @@ check discovery → target qualification → per-target observation
 - `src/report/` renders terminal, self-contained HTML, and bounded GitHub job-summary reports from the same typed report object. The GitHub renderer is a presentation projection only and cannot add evidence.
 - `src/analyze.ts` orchestrates the pipeline and exposes the public API.
 
+Before diff extraction, `src/git.ts` validates a bounded NUL-delimited index inventory, including merge stages and cached-stat flags. Unresolved merges and `assume-unchanged`/`skip-worktree` entries abort all selection modes rather than allowing Git to hide inputs consumed by filesystem-backed analysis. The index is never rewritten. On POSIX, a timeout waits through the one-second TERM-to-KILL grace period even if the parent closes first, so descendants with redirected output cannot cancel process-group escalation. Windows retains its separate `taskkill /T /F` completion boundary.
+
 ## Design decisions
 
 ### Local static relationships, not runtime coverage
diff --git a/CHANGELOG.md b/CHANGELOG.md
index e6bf8fc..cfdc870 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,8 @@ All notable changes are documented here. This project follows Semantic Versionin
 
 ### Fixed
 
+- Rejected unresolved merge stages and `assume-unchanged`/`skip-worktree` index entries before diff evidence or repository checks in every selection mode. Hidden modifications and sparse-checkout omissions now produce actionable errors instead of misleading empty or snapshot-aligned reports; the index is never modified.
+- Preserved POSIX timeout escalation after a parent exits, preventing descendants with redirected output and a TERM handler from surviving cancellation of the KILL timer. Windows process-tree termination remains unchanged.
 - Repaired the dogfood gate by moving test preparation into npm's `pretest` lifecycle and retaining a direct serial `node --test` command. It now requires positive observations for every related compiled target while correctly retaining partial evidence for filename-mapped TypeScript source. Added a self-discovery regression and a PR CI dogfood step; shell-chain recognition and compiled-source confidence remain conservative.
 - Unified static Git execution so immutable workspace checks and test-map snapshot reads receive the same helper suppression as diff inspection. Driver discovery now includes worktree configuration, refreshes on each operation, uses NUL-delimited names, and fails closed when incomplete.
 - Rejected truncated, timed-out, or failed Git reads instead of treating partial paths or patches as complete evidence. Per-file patch failures now stop analysis with exit code 2.
diff --git a/README.md b/README.md
index cd8dbcd..5ab4bf2 100644
--- a/README.md
+++ b/README.md
@@ -109,6 +109,8 @@ The released composite Action is available at `hzw0813/proofdiff@v0.5.3`. Use th
 
 For immutable `--base`, `--range`, and `--staged` analysis, v0.5.3 conservatively binds filesystem-backed analysis to the selected Git state instead of mixing snapshots. Base/range analysis requires the selected target to be the checked-out `HEAD`; staged analysis requires tracked worktree content to match the index. Git-visible untracked inputs and ignored metadata/test inputs that could affect static discovery fail closed. With `--run-checks`, ignored repository-local runtime inputs are rejected more broadly because repository commands could consume them; bounded dependency/cache directories remain environment inputs. An explicitly supplied LCOV file can be accepted as that exact data artifact under its separate commit-binding checks, but it does not authorize sibling files.
 
+All diff modes also require a resolved index without `assume-unchanged` or `skip-worktree` entries. These flags can hide modified or missing source, configuration, and tests from Git while ProofDiff reads the filesystem. Unresolved merges and sparse checkouts therefore stop with an actionable error (CLI exit 2, even with `--fail-on never`) before checks run or a report is written. Resolve and stage conflicts, use a full checkout (`git sparse-checkout disable`), or clear manually set flags with `git update-index --no-assume-unchanged --no-skip-worktree -- <path>`. ProofDiff never clears flags or expands the checkout itself.
+
 The released Action writes a concise, bounded **ProofDiff · Change Evidence** job summary by default, so reviewers can see changed-file evidence without opening logs. It uses the same report as terminal/JSON/HTML output, requires no write token, and does not create PR comments. Full provenance remains in the log and optional HTML artifact.
 
 ## Useful commands
diff --git a/SECURITY.md b/SECURITY.md
index 9c91808..4fe4ef9 100644
--- a/SECURITY.md
+++ b/SECURITY.md
@@ -42,6 +42,10 @@ Runner qualification is static and data-only. pytest configuration reads are bou
 
 These measures are defense in depth, **not a sandbox**. A command can still read accessible files, use the network, spawn processes, exploit installed tools, or persist outside the repository. Use a disposable VM/container with network and secrets removed when executing checks from untrusted contributions. On pull requests from forks, keep `run-checks: false` unless the code has been reviewed.
 
+POSIX timeout cleanup sends TERM to the process group and preserves the one-second KILL escalation even after the direct child exits and its output pipes close. This covers ordinary descendants with redirected output; descendants that deliberately leave the process group remain outside that mechanism. Windows uses its existing native process-tree termination. These mechanisms do not promise containment of arbitrary programs.
+
+All selections reject unresolved index merge stages and `assume-unchanged`/`skip-worktree` entries before check execution. Otherwise Git can report an aligned snapshot while filesystem-backed discovery reads different or missing code. Sparse checkouts must be expanded by the user or analyzed in a full separate checkout; static inspection never modifies the user's index flags.
+
 ## Data handling
 
 Terminal, JSON, and HTML reports can contain repository paths, symbol names, relationships, target-qualification reasons, per-target counts, check commands, and bounded check output. Owned inline observer source is abbreviated in the HTML command display but remains present in machine-readable JSON for reproducibility. Treat reports as repository-sensitive artifacts. The HTML report is self-contained, loads no remote resources, and has a restrictive Content Security Policy, but anyone receiving it can read its contents. The shorter GitHub job summary still contains changed and test-target paths; users with access to the workflow run can read them.
diff --git a/dist/git.d.ts.map b/dist/git.d.ts.map
index cd83463..f6777b7 100644
--- a/dist/git.d.ts.map
+++ b/dist/git.d.ts.map
@@ -1 +1 @@
-{"version":3,"file":"git.d.ts","sourceRoot":"","sources":["../src/git.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,WAAW,EAAwB,aAAa,EAAE,cAAc,EAAE,MAAM,YAAY,CAAC;AAGnG,OAAO,EAAE,QAAQ,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AAW3D,wBAAsB,cAAc,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CASnE;AAmBD,wBAAsB,qBAAqB,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CAKxF;AAED,wBAAsB,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,SAAS,EAAE,aAAa,GAAG,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,CAQrG;AAWD,wBAAsB,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE;IAAE,IAAI,CAAC,EAAE,MAAM,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAC;IAAC,MAAM,CAAC,EAAE,OAAO,CAAA;CAAE,GAAG,OAAO,CAAC;IAAE,SAAS,EAAE,aAAa,CAAC;IAAC,IAAI,EAAE,MAAM,EAAE,CAAA;CAAE,CAAC,CA+BlK;AAwFD,wBAAsB,YAAY,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,EAAE,gBAAgB,EAAE,OAAO,EAAE,cAAc,CAAC,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,WAAW,EAAE,CAAC,CAuCjJ;AAED,wBAAsB,kBAAkB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,CAMxE;AAED,wBAAsB,mBAAmB,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,SAAQ,GAAG,OAAO,CAAC;IAAE,KAAK,EAAE,MAAM,EAAE,CAAC;IAAC,SAAS,EAAE,OAAO,CAAA;CAAE,CAAC,CAQvH;AAED,wBAAsB,cAAc,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,CAW1E"}
\ No newline at end of file
+{"version":3,"file":"git.d.ts","sourceRoot":"","sources":["../src/git.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,WAAW,EAAwB,aAAa,EAAE,cAAc,EAAE,MAAM,YAAY,CAAC;AAGnG,OAAO,EAAE,QAAQ,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AAqC3D,wBAAsB,cAAc,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CASnE;AAmBD,wBAAsB,qBAAqB,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CAKxF;AAED,wBAAsB,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,SAAS,EAAE,aAAa,GAAG,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,CAQrG;AAWD,wBAAsB,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE;IAAE,IAAI,CAAC,EAAE,MAAM,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAC;IAAC,MAAM,CAAC,EAAE,OAAO,CAAA;CAAE,GAAG,OAAO,CAAC;IAAE,SAAS,EAAE,aAAa,CAAC;IAAC,IAAI,EAAE,MAAM,EAAE,CAAA;CAAE,CAAC,CA+BlK;AAwFD,wBAAsB,YAAY,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,EAAE,gBAAgB,EAAE,OAAO,EAAE,cAAc,CAAC,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,WAAW,EAAE,CAAC,CAwCjJ;AAED,wBAAsB,kBAAkB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,CAMxE;AAED,wBAAsB,mBAAmB,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,SAAQ,GAAG,OAAO,CAAC;IAAE,KAAK,EAAE,MAAM,EAAE,CAAC;IAAC,SAAS,EAAE,OAAO,CAAA;CAAE,CAAC,CAQvH;AAED,wBAAsB,cAAc,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,CAW1E"}
\ No newline at end of file
diff --git a/dist/git.js b/dist/git.js
index 8c011cf..627537d 100644
--- a/dist/git.js
+++ b/dist/git.js
@@ -10,6 +10,35 @@ async function git(root, args, allowFailure = false) {
     }
     return result.stdout;
 }
+/** Git's cached stat flags must not hide inputs that filesystem-backed analysis reads. */
+async function assertInspectableIndex(root) {
+    const output = await git(root, ["ls-files", "--stage", "-v", "-z"]);
+    const conflicts = [];
+    const hidden = [];
+    if (output !== "" && !output.endsWith("\0"))
+        throw new GitError("Incomplete Git index inventory; cannot establish evidence.");
+    for (const record of output.split("\0").filter(Boolean)) {
+        // Parse only the fixed prefix; paths may contain tabs, newlines, and literal backslashes.
+        const entry = record.match(/^([A-Za-z?]) [0-7]{6} (?:[0-9a-f]{40}|[0-9a-f]{64}) ([0-3])\t([\s\S]+)$/);
+        if (!entry)
+            throw new GitError("Unrecognized Git index record; cannot establish evidence.");
+        const [, tag, stage, file] = entry;
+        if (stage !== "0")
+            conflicts.push(file);
+        if (tag === "S" || tag !== tag.toUpperCase())
+            hidden.push(file);
+    }
+    const detail = (files) => {
+        const paths = unique(files);
+        return `${paths.slice(0, 5).map((file) => JSON.stringify(file)).join(", ")}${paths.length > 5 ? `, and ${paths.length - 5} more` : ""}`;
+    };
+    if (conflicts.length > 0) {
+        throw new GitError(`The Git index contains unresolved merge stages: ${detail(conflicts)}. Resolve and stage the conflicts (or abort the merge) before analysis; combined conflict diffs cannot establish a single source snapshot.`);
+    }
+    if (hidden.length > 0) {
+        throw new GitError(`The Git index contains assume-unchanged or skip-worktree entries: ${detail(hidden)}. Those flags can hide changed or missing filesystem inputs. Use a full checkout (git sparse-checkout disable for sparse checkouts), or clear the flags with git update-index --no-assume-unchanged --no-skip-worktree -- <path>, then retry. ProofDiff does not modify the index.`);
+    }
+}
 export async function findRepository(value) {
     const candidate = await resolveRepositoryPath(value);
     const result = await gitResult(candidate, ["rev-parse", "--show-toplevel"]);
@@ -184,6 +213,7 @@ function changeKind(status) {
     }
 }
 export async function changedFiles(root, diffArgs, includeUntracked, knownUntracked) {
+    await assertInspectableIndex(root);
     const safeDiffOptions = ["--no-ext-diff", "--no-textconv", "--ignore-submodules=all"];
     const status = parseNameStatus(await git(root, ["diff", ...safeDiffOptions, "--name-status", "-z", "--find-renames", ...diffArgs, "--"]));
     const stats = parseNumstat(await git(root, ["diff", ...safeDiffOptions, "--numstat", "-z", "--find-renames", ...diffArgs, "--"]));
diff --git a/dist/git.js.map b/dist/git.js.map
index 08fbdd4..2d4ec92 100644
--- a/dist/git.js.map
+++ b/dist/git.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/dist/process.d.ts.map b/dist/process.d.ts.map
index e0ce1da..be6b23f 100644
--- a/dist/process.d.ts.map
+++ b/dist/process.d.ts.map
@@ -1 +1 @@
-{"version":3,"file":"process.d.ts","sourceRoot":"","sources":["../src/process.ts"],"names":[],"mappings":"AAIA,MAAM,WAAW,aAAa;IAC5B,QAAQ,EAAE,MAAM,GAAG,IAAI,CAAC;IACxB,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,OAAO,CAAC;IAClB,UAAU,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,OAAO,CAAC;IACnB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,oBAAoB,CAAC,EAAE,OAAO,CAAC;IAC/B,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,cAAc;IAC7B,GAAG,EAAE,MAAM,CAAC;IACZ,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,GAAG,CAAC,EAAE,MAAM,CAAC,UAAU,CAAC;IACxB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,mBAAmB,CAAC,EAAE,MAAM,CAAC;CAC9B;AAED,wBAAsB,UAAU,CAAC,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,EAAE,OAAO,EAAE,cAAc,GAAG,OAAO,CAAC,aAAa,CAAC,CA6KjH;AAED,wBAAgB,kBAAkB,IAAI,MAAM,CAK3C;AAED,wBAAgB,2BAA2B,IAAI,MAAM,CAAC,UAAU,CAc/D"}
\ No newline at end of file
+{"version":3,"file":"process.d.ts","sourceRoot":"","sources":["../src/process.ts"],"names":[],"mappings":"AAIA,MAAM,WAAW,aAAa;IAC5B,QAAQ,EAAE,MAAM,GAAG,IAAI,CAAC;IACxB,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,OAAO,CAAC;IAClB,UAAU,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,OAAO,CAAC;IACnB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,oBAAoB,CAAC,EAAE,OAAO,CAAC;IAC/B,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,cAAc;IAC7B,GAAG,EAAE,MAAM,CAAC;IACZ,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,GAAG,CAAC,EAAE,MAAM,CAAC,UAAU,CAAC;IACxB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,mBAAmB,CAAC,EAAE,MAAM,CAAC;CAC9B;AAED,wBAAsB,UAAU,CAAC,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,EAAE,OAAO,EAAE,cAAc,GAAG,OAAO,CAAC,aAAa,CAAC,CAkLjH;AAED,wBAAgB,kBAAkB,IAAI,MAAM,CAK3C;AAED,wBAAgB,2BAA2B,IAAI,MAAM,CAAC,UAAU,CAc/D"}
\ No newline at end of file
diff --git a/dist/process.js b/dist/process.js
index 117b2c1..0615ed0 100644
--- a/dist/process.js
+++ b/dist/process.js
@@ -18,6 +18,7 @@ export async function runProcess(command, args, options) {
         let childExitCode = null;
         let windowsTerminationComplete = false;
         let windowsTerminationError;
+        let posixTerminationError;
         let timer;
         let terminationFallback;
         const child = spawn(command, args, {
@@ -86,6 +87,9 @@ export async function runProcess(command, args, options) {
             if (timedOut && process.platform === "win32") {
                 windowsTerminationError ??= error.message;
             }
+            else if (timedOut) {
+                posixTerminationError ??= error.message;
+            }
             else {
                 finish(null, error.message);
             }
@@ -101,9 +105,11 @@ export async function runProcess(command, args, options) {
                 childExitCode = code;
                 finishWindowsTimeoutIfComplete();
             }
-            else {
+            else if (!timedOut) {
                 finish(code);
             }
+            // On POSIX, parent close says nothing about descendants with redirected
+            // stdio. Keep the timeout escalation alive until the process group is killed.
         });
         if (options.stdin !== undefined) {
             // A parser can exit before consuming its input. Wait for close/timeout, but never
@@ -116,7 +122,7 @@ export async function runProcess(command, args, options) {
                 return;
             closeChildStreams();
             child.unref();
-            finish(null, error);
+            finish(null, error ?? posixTerminationError);
         };
         const scheduleForcedFinish = (error, delayMs = 1_000) => {
             if (settled)
diff --git a/dist/process.js.map b/dist/process.js.map
index 06242a4..986afb9 100644
--- a/dist/process.js.map
+++ b/dist/process.js.map
@@ -1 +1 @@
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\ No newline at end of file
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diff --git a/docs/production-readiness-audit.md b/docs/production-readiness-audit.md
index 143b1d4..99cec37 100644
--- a/docs/production-readiness-audit.md
+++ b/docs/production-readiness-audit.md
@@ -37,3 +37,17 @@ The repository's `lint` command is TypeScript typechecking, not a separate styli
 - Dependency major-version PRs are separate compatibility decisions and were not merged by this audit.
 
 This is a tested hardening pass, not a claim that every real-world repository or threat has been verified.
+
+## Follow-up after PR #69
+
+Baseline: current main `9b886a25abe7f809112c13d26184ed28cc5b173b`. The downloaded text files were checked against that commit's Git blob identities before editing. This follow-up examined the remaining filesystem-alignment assumptions and process lifetime boundary. Six new regression cases reproduced five failures against the baseline; the inherited-output descendant case already passed and now protects the existing behavior.
+
+| Priority | Reproduced weakness | Fix and regression coverage |
+| --- | --- | --- |
+| High | `assume-unchanged` and `skip-worktree` hid a modified source file from `git diff`; immutable analysis accepted it as aligned and reported no changes. | Read index stages and flags as bounded NUL-delimited data before diff extraction. Reject hidden inputs in working-tree, base, range, and staged modes before checks run. Tests assert exit 2 even under `--fail-on never`, no new report or execution marker, preserved flags, and successful analysis after the caller clears flags. |
+| High | A real sparse-index checkout with absent source/test paths passed immutable analysis. An unresolved merge also reached analysis and execution despite lacking a single resolved snapshot. | Reject sparse/skip-worktree entries and nonzero merge stages with recovery guidance. Regressions create a real cone-mode sparse index and a conflicting merge, including all four selection modes for conflicts. |
+| Medium | A timed-out POSIX parent exited and closed its pipes, cancelling the escalation timer while a TERM-resistant descendant with redirected output kept running. | Parent close no longer completes a POSIX timeout before process-group KILL escalation. Real-process tests check that a descendant heartbeat stops with both redirected and inherited output. Windows retains its native termination path. |
+
+These changes add no dependencies, runtime network access, telemetry, uploads, or automatic check execution. They do not strengthen verification statuses or change schema `1.0`. Sparse checkouts are deliberately rejected rather than claimed supported; use a full checkout. Even clean flagged entries are rejected because cached Git stat assumptions cannot independently establish filesystem alignment. The index inventory uses the existing 8 MB output bound and fails closed if incomplete. No index flags or checkout contents are changed by inspection.
+
+The expanded suite contains 176 tests, including two new POSIX-only process tests. Full validation outcomes, including the existing Linux/macOS/Windows × Node 22/24/26 matrix, are recorded in the draft PR. Remaining work includes the submodule visibility limitation above, broader bounded runner/monorepo support, and isolated snapshot analysis. Process-group cleanup remains best effort: deliberately detached descendants and arbitrary repository code require an external OS sandbox. Concurrent repository mutation remains outside this pass.
diff --git a/docs/verification-model.md b/docs/verification-model.md
index 4d99219..d905b60 100644
--- a/docs/verification-model.md
+++ b/docs/verification-model.md
@@ -6,6 +6,8 @@ ProofDiff answers “what evidence exists?” It does not answer “is this safe
 
 Facts are directly observed: Git changed a path, a parser found a declaration or name-only call site, a user supplied a specific source-to-test declaration, or a command exited with a particular code. Call sites are filtered to changed lines and do not claim target resolution or runtime execution.
 
+Before reading diff evidence, every selection requires a resolved Git index without `assume-unchanged` or `skip-worktree` entries. A bounded NUL-delimited index inventory checks flags and merge stages independently of `git diff`'s cached filesystem assumptions. Hidden entries (including sparse checkout) and unresolved merges abort analysis before repository execution; they cannot yield a successful empty-change report. This conservative precondition applies even if a flagged file currently appears unchanged. It does not mutate the index and does not provide concurrent filesystem isolation.
+
 Static relationships are reproducible but incomplete: file A imports file B; a test reaches a changed file through resolvable local imports. They are labeled medium confidence because they do not show that a runtime path executed.
 
 For JavaScript/TypeScript, “resolvable local imports” includes relative paths plus two bounded metadata-backed subsets: exact/single-wildcard compiler `paths` mappings and exact self-references through the importing package's own `name` and `exports`. A matched `paths` target is resolved only through documented explicit-extension substitution, or through extensionless file/index lookup when Bundler or Node10 is explicitly configured. NodeNext-family extensionless lookup is context-sensitive and remains unresolved. ProofDiff records the metadata path, matched key, mechanism, target, and limitation internally. This stronger static evidence does not say that a runtime, bundler, or test runner used the same mapping.
diff --git a/src/git.ts b/src/git.ts
index 8ca69bd..c32a534 100644
--- a/src/git.ts
+++ b/src/git.ts
@@ -14,6 +14,32 @@ async function git(root: string, args: string[], allowFailure = false): Promise<
   return result.stdout;
 }
 
+/** Git's cached stat flags must not hide inputs that filesystem-backed analysis reads. */
+async function assertInspectableIndex(root: string): Promise<void> {
+  const output = await git(root, ["ls-files", "--stage", "-v", "-z"]);
+  const conflicts: string[] = [];
+  const hidden: string[] = [];
+  if (output !== "" && !output.endsWith("\0")) throw new GitError("Incomplete Git index inventory; cannot establish evidence.");
+  for (const record of output.split("\0").filter(Boolean)) {
+    // Parse only the fixed prefix; paths may contain tabs, newlines, and literal backslashes.
+    const entry = record.match(/^([A-Za-z?]) [0-7]{6} (?:[0-9a-f]{40}|[0-9a-f]{64}) ([0-3])\t([\s\S]+)$/);
+    if (!entry) throw new GitError("Unrecognized Git index record; cannot establish evidence.");
+    const [, tag, stage, file] = entry as [string, string, string, string];
+    if (stage !== "0") conflicts.push(file);
+    if (tag === "S" || tag !== tag.toUpperCase()) hidden.push(file);
+  }
+  const detail = (files: string[]): string => {
+    const paths = unique(files);
+    return `${paths.slice(0, 5).map((file) => JSON.stringify(file)).join(", ")}${paths.length > 5 ? `, and ${paths.length - 5} more` : ""}`;
+  };
+  if (conflicts.length > 0) {
+    throw new GitError(`The Git index contains unresolved merge stages: ${detail(conflicts)}. Resolve and stage the conflicts (or abort the merge) before analysis; combined conflict diffs cannot establish a single source snapshot.`);
+  }
+  if (hidden.length > 0) {
+    throw new GitError(`The Git index contains assume-unchanged or skip-worktree entries: ${detail(hidden)}. Those flags can hide changed or missing filesystem inputs. Use a full checkout (git sparse-checkout disable for sparse checkouts), or clear the flags with git update-index --no-assume-unchanged --no-skip-worktree -- <path>, then retry. ProofDiff does not modify the index.`);
+  }
+}
+
 export async function findRepository(value: string): Promise<string> {
   const candidate = await resolveRepositoryPath(value);
   const result = await gitResult(candidate, ["rev-parse", "--show-toplevel"]);
@@ -188,6 +214,7 @@ function changeKind(status: string): ChangeKind {
 }
 
 export async function changedFiles(root: string, diffArgs: string[], includeUntracked: boolean, knownUntracked?: string[]): Promise<ChangedFile[]> {
+  await assertInspectableIndex(root);
   const safeDiffOptions = ["--no-ext-diff", "--no-textconv", "--ignore-submodules=all"];
   const status = parseNameStatus(await git(root, ["diff", ...safeDiffOptions, "--name-status", "-z", "--find-renames", ...diffArgs, "--"]));
   const stats = parseNumstat(await git(root, ["diff", ...safeDiffOptions, "--numstat", "-z", "--find-renames", ...diffArgs, "--"]));
diff --git a/src/process.ts b/src/process.ts
index 52a27c7..a3c8cf1 100644
--- a/src/process.ts
+++ b/src/process.ts
@@ -41,6 +41,7 @@ export async function runProcess(command: string, args: string[], options: Proce
     let childExitCode: number | null = null;
     let windowsTerminationComplete = false;
     let windowsTerminationError: string | undefined;
+    let posixTerminationError: string | undefined;
     let timer: NodeJS.Timeout | undefined;
     let terminationFallback: NodeJS.Timeout | undefined;
 
@@ -109,6 +110,8 @@ export async function runProcess(command: string, args: string[], options: Proce
     child.on("error", (error) => {
       if (timedOut && process.platform === "win32") {
         windowsTerminationError ??= error.message;
+      } else if (timedOut) {
+        posixTerminationError ??= error.message;
       } else {
         finish(null, error.message);
       }
@@ -123,9 +126,11 @@ export async function runProcess(command: string, args: string[], options: Proce
         childExited = true;
         childExitCode = code;
         finishWindowsTimeoutIfComplete();
-      } else {
+      } else if (!timedOut) {
         finish(code);
       }
+      // On POSIX, parent close says nothing about descendants with redirected
+      // stdio. Keep the timeout escalation alive until the process group is killed.
     });
 
     if (options.stdin !== undefined) {
@@ -139,7 +144,7 @@ export async function runProcess(command: string, args: string[], options: Proce
       if (settled) return;
       closeChildStreams();
       child.unref();
-      finish(null, error);
+      finish(null, error ?? posixTerminationError);
     };
 
     const scheduleForcedFinish = (error?: string, delayMs = 1_000): void => {
diff --git a/tests/process.test.ts b/tests/process.test.ts
index 1e198c8..531db28 100644
--- a/tests/process.test.ts
+++ b/tests/process.test.ts
@@ -1,6 +1,49 @@
 import assert from "node:assert/strict";
 import test from "node:test";
+import { readFile, rm } from "node:fs/promises";
+import path from "node:path";
+import { setTimeout as delay } from "node:timers/promises";
 import { runProcess } from "../src/process.js";
+import { temporaryDirectory } from "./helpers.js";
+
+for (const inheritedOutput of [false, true]) {
+  test(`timeout kills a TERM-resistant descendant after its parent exits (inherited output: ${inheritedOutput})`, { skip: process.platform === "win32" }, async (context) => {
+    const root = await temporaryDirectory();
+    let descendantPid: number | undefined;
+    context.after(async () => {
+      if (descendantPid !== undefined) {
+        try { process.kill(descendantPid, "SIGKILL"); } catch { /* Already terminated. */ }
+      }
+      await rm(root, { recursive: true, force: true });
+    });
+    const descendant = `
+      const fs = require('node:fs');
+      process.on('SIGTERM', () => {});
+      let ticks = 0;
+      setInterval(() => fs.writeFileSync('heartbeat', String(++ticks)), 20);
+      fs.writeFileSync('pid', String(process.pid));
+      process.send('ready');
+    `;
+    const parent = `
+      const { spawn } = require('node:child_process');
+      const child = spawn(process.execPath, ['-e', ${JSON.stringify(descendant)}], {
+        stdio: ['ignore', ${inheritedOutput ? "'inherit', 'inherit'" : "'ignore', 'ignore'"}, 'ipc']
+      });
+      child.on('message', () => console.log('ready'));
+      setInterval(() => {}, 1000);
+    `;
+    const result = await runProcess(process.execPath, ["-e", parent], { cwd: root, timeoutMs: 2_500 });
+    descendantPid = Number(await readFile(path.join(root, "pid"), "utf8"));
+    assert.equal(result.stdout.trim(), "ready", "descendant must install its TERM handler before timeout");
+    assert.equal(result.timedOut, true);
+    assert.ok(result.durationMs < 6_000, `timeout took ${result.durationMs} ms`);
+    // Allow any in-flight write to finish; a surviving descendant continues ticking.
+    await delay(100);
+    const stopped = await readFile(path.join(root, "heartbeat"), "utf8");
+    await delay(150);
+    assert.equal(await readFile(path.join(root, "heartbeat"), "utf8"), stopped);
+  });
+}
 
 test("an early stdin close reports an input error without crashing ProofDiff", async () => {
   const result = await runProcess(process.execPath, ["-e", "process.exit(0)"], {
diff --git a/tests/selection-workspace.test.ts b/tests/selection-workspace.test.ts
index 4d18650..6eba0e1 100644
--- a/tests/selection-workspace.test.ts
+++ b/tests/selection-workspace.test.ts
@@ -4,7 +4,7 @@ import { rm } from "node:fs/promises";
 import test from "node:test";
 import { analyzeRepository } from "../src/analyze.js";
 import { pathExists } from "../src/util.js";
-import { git, initializeRepository, writeFiles } from "./helpers.js";
+import { git, initializeRepository, runCli, writeFiles } from "./helpers.js";
 
 const fixture = {
   "package.json": JSON.stringify({ name: "selection-binding", private: true, type: "module", scripts: { test: "node --test" } }, null, 2),
@@ -12,6 +12,59 @@ const fixture = {
   "test/value.test.js": "import test from 'node:test'; import assert from 'node:assert/strict'; import { value } from '../src/value.js'; test('value', () => assert.equal(value, 1));\n",
 };
 
+for (const flag of ["assume-unchanged", "skip-worktree"]) {
+  test(`${flag} cannot hide filesystem changes from any selection or authorize checks`, async (context) => {
+    const root = await initializeRepository({
+      ...fixture,
+      "probe.cjs": "require('node:fs').writeFileSync('probe-ran', 'yes');\n",
+      "package.json": JSON.stringify({ scripts: { test: "node probe.cjs" } }),
+    });
+    context.after(() => rm(root, { recursive: true, force: true }));
+    git(root, "update-index", `--${flag}`, "src/value.js");
+    await writeFiles(root, { "src/value.js": "export const value = 999;\n" });
+    for (const selection of [{}, { base: "HEAD" }, { range: "HEAD..HEAD" }, { staged: true }]) {
+      await assert.rejects(analyzeRepository({ repo: root, ...selection, runChecks: true }), new RegExp(flag));
+    }
+    assert.equal(await pathExists(path.join(root, "probe-ran")), false);
+    const cli = runCli(["--repo", root, "--json", "--output", path.join(root, "report.json"), "--fail-on", "never"]);
+    assert.equal(cli.status, 2);
+    assert.match(cli.stderr, new RegExp(flag));
+    assert.equal(await pathExists(path.join(root, "report.json")), false);
+    // Inspection must not clear flags or rewrite the user's index.
+    assert.match(git(root, "ls-files", "-v", "src/value.js"), flag === "skip-worktree" ? /^S / : /^h /);
+    git(root, "update-index", `--no-${flag}`, "src/value.js");
+    const report = await analyzeRepository({ repo: root });
+    assert.deepEqual(report.assessments.map((item) => item.file.path), ["src/value.js"]);
+  });
+}
+
+test("sparse checkouts fail closed with a recovery diagnostic for missing source inputs", async (context) => {
+  const root = await initializeRepository({ ...fixture, "other/module.js": "export const other = 1;\n" });
+  context.after(() => rm(root, { recursive: true, force: true }));
+  git(root, "sparse-checkout", "set", "--cone", "--sparse-index", "src");
+  await assert.rejects(analyzeRepository({ repo: root, base: "HEAD" }), /skip-worktree.*full checkout/s);
+});
+
+test("unresolved merge stages cannot produce reports or execute checks", async (context) => {
+  const root = await initializeRepository({
+    ...fixture,
+    "probe.cjs": "require('node:fs').writeFileSync('probe-ran', 'yes');\n",
+    "package.json": JSON.stringify({ scripts: { test: "node probe.cjs" } }),
+  });
+  context.after(() => rm(root, { recursive: true, force: true }));
+  const branch = git(root, "symbolic-ref", "--short", "HEAD").trim();
+  git(root, "checkout", "-qb", "conflict-side");
+  await commitChange(root, "export const value = 2;\n", "side");
+  git(root, "checkout", "-q", branch);
+  await commitChange(root, "export const value = 3;\n", "main");
+  assert.throws(() => git(root, "merge", "conflict-side"));
+  for (const selection of [{}, { base: "HEAD" }, { range: "HEAD..HEAD" }, { staged: true }]) {
+    await assert.rejects(analyzeRepository({ repo: root, ...selection, runChecks: true }), /unresolved merge.*src\/value\.js/s);
+  }
+  assert.match(git(root, "ls-files", "--unmerged"), /src\/value\.js/);
+  assert.equal(await pathExists(path.join(root, "probe-ran")), false);
+});
+
 test("all immutable static modes suppress configured Git clean filters", async (context) => {
   const root = await initializeRepository({
     ".gitattributes": "*.txt filter=probe\n",