diff --git a/docs/adr/2264-golden-parity-redesign.md b/docs/adr/2264-golden-parity-redesign.md
index 279686793..0702f09c9 100644
--- a/docs/adr/2264-golden-parity-redesign.md
+++ b/docs/adr/2264-golden-parity-redesign.md
@@ -76,3 +76,18 @@ Only the **transformed** outputs (per-runtime projections from `runtime-artifact
 - ADR-1239 (Phase B safety net); issues #2086, #2095, #2100, #2117, #1691
 - Node.js test runner: `context.assert.snapshot` + `--test-update-snapshots`
 - Jest `--ci` snapshot posture (fail on new snapshot, deliberate `-u` regeneration)
+
+## Amendment (2026-07-14): Phase 2 redesign — the copy/transform split was unsound
+
+Implementing Phase 2 began with an empirical spike classifying every emitted install file. It **overturned the §2–§4 premise**:
+
+- **The copy/transform boundary is not clean.** Nearly every emitted file passes through a *deterministic* rewrite (path-prefix canonicalization, `{{GSD_VERSION}}` stamping, hyphen-normalization) — even for claude, the reference host. Only ~36% of claude's files are byte-identical to source; ~64% are "transformed." A "content-hash only the transformed ~5%" golden (§4) was the wrong model.
+- **The §3 from-source copy-parity property test is unsound.** Asserting `emitted == transform(source)` by calling the installer's own transform functions is largely tautological (it catches only non-determinism) — strictly *weaker* regression coverage than the current golden. Making it independent means reimplementing the transform in the test — the exact duplication this epic fights. It is also noisier than the golden it replaces: the harness's `configDir == $HOME` collapses path canonicalization differently than a real install, mis-classifying ~147 of claude's files as transforms.
+- **The real defect was stale fixtures, not platform divergence.** The Phase-1 red (`gsd-statusline.js` + 3 claude-local files) was *deterministic* (macOS hash == Linux-bench hash for every entry); the fixtures were simply stale because `golden-install-parity` was not selected by CI when the emitting source (a `hooks/` file) changed, so it merged undetected.
+
+**Revised Phase 2 (implemented in #2267):**
+
+1. **File-set snapshot** — `tests/golden-install-tree.test.cjs` + `tests/fixtures/install-tree/*.json`: a per-runtime sorted list of emitted paths (no hashes), reusing the single-source exclusions via `buildInstallTree` (= sorted keys of `buildParityManifest`). Cheap structural coverage; changes only when the file *set* changes, giving a clean reviewable diff instead of hash noise.
+2. **Anti-staleness CI selection** — `scripts/ci-test-scope.cjs` gains a rule selecting `golden-install-parity` + the file-set snapshot whenever an installed-source path changes: the four `gsd-core/` content subtrees (`workflows`, `templates`, `references`, `contexts`) + `gsd-core/bin/shared/*.json`, plus `hooks/**`, `commands/**`, `agents/**`, `skills/**`, and the shipped `scripts/*` files (`scripts/changeset/`, `scripts/lib/`, and three named generators) — not just `src/`/installer paths. `gsd-core/bin/**` (tsc-compiled) is deliberately excluded (already covered by the installer rule). This makes the #2266 silent-staleness class impossible: a source edit that changes emitted output re-verifies the fixtures at PR time.
+
+**Deferred as an optional future refinement:** the §3-style content-dedup of verbatim copies. The *safe* subset (structurally raw-copied non-`.md`/`.js` data files) is modest, and the broad form is unsound — a `.md` file that is byte-equal today transforms the moment a self-reference is added, producing false property-test failures. Since the anti-staleness rule already removes the root pain (silent stale merges) and the file-set snapshot adds structural coverage, the content-hash golden is retained as-is; churn on *transformed* output is legitimate (you should review transformed output when you change its source).
diff --git a/scripts/ci-test-scope.cjs b/scripts/ci-test-scope.cjs
index bdc7ac92d..dc06bb3db 100644
--- a/scripts/ci-test-scope.cjs
+++ b/scripts/ci-test-scope.cjs
@@ -145,6 +145,37 @@ const RULES = [
       'tests/golden-install-parity.test.cjs', // any src/installer change can alter emitted install artifacts → re-verify golden install parity (drift guard)
     ],
   },
+  {
+    name: 'shipped install content (golden-parity drift guard, #2267)',
+    // Every source file the installer EMITS into a runtime layout is captured by
+    // golden-install-parity + the install-tree snapshot. A source edit here that
+    // changes emitted output MUST re-verify the fixtures — otherwise stale golden
+    // fixtures merge silently (#2266: a hooks/gsd-statusline.js edit changed
+    // installed output but no rule selected golden-parity, so stale fixtures
+    // shipped to next undetected). Union semantics: this ADDS the parity guard on
+    // top of each path's existing content-specific tests. Targeted lane only (the
+    // golden test skips win32 by design), no fullMatrix.
+    // NOTE: intentionally NOT a blanket 'gsd-core/' prefix, for two reasons:
+    // (1) gsd-core/bin/** is tsc-compiled runtime output — EXCLUDED_PREFIXES-
+    //     excluded from both manifests, and already covered by the 'installer and
+    //     package layout' rule (path.startsWith('gsd-core/bin/')) — so matching it
+    //     here would be pure noise; and
+    // (2) enumerating only the installer-shipped content subtrees preserves the
+    //     bug-408 unit-fallback contract: a gsd-core/ path that is NOT shipped
+    //     verbatim (the bug-408 test uses gsd-core/src/some-util.js) must still
+    //     fall back to ['unit'] when no rule matches.
+    // Listed: the four gsd-core content subtrees the installer ships verbatim
+    // (contexts, references, templates, workflows) + bin/shared/*.json data files.
+    // Verify against Object.keys(golden fixture) grouped by gsd-core/<subdir>.
+    match: path =>
+      ['hooks/', 'commands/', 'agents/', 'skills/', 'gsd-core/workflows/', 'gsd-core/templates/', 'gsd-core/references/', 'gsd-core/contexts/', 'scripts/changeset/', 'scripts/lib/'].some(p => path.startsWith(p)) ||
+      (path.startsWith('gsd-core/bin/shared/') && path.endsWith('.json')) ||
+      ['scripts/fix-slash-commands.cjs', 'scripts/gen-capability-registry.cjs', 'scripts/gen-loop-host-contract.cjs'].includes(path),
+    tests: [
+      'tests/golden-install-parity.test.cjs',
+      'tests/golden-install-tree.test.cjs',
+    ],
+  },
   {
     name: 'hooks',
     match: path => path.startsWith('hooks/'),
@@ -364,8 +395,15 @@ function classify(files) {
   for (const file of files) {
     // Determine if this file is product/pipeline code.
     // docs/ and root-level .md files are intentionally excluded.
+    // 'skills/' is shipped agent-skill content installed into every runtime by
+    // the installer (see the 'shipped install content' RULES entry below) — it
+    // must be product code, or a skills/-only change silently gets
+    // code_changed=false and skips the ENTIRE CI matrix, not merely golden-parity
+    // (found while verifying the #2267 golden-parity rule against skills/**: the
+    // rule fired in `reasons` but classify()'s codeChanged gate zeroed out every
+    // targeted test because 'skills/' was absent from this list).
     if (
-      ['bin/', 'src/', 'gsd-core/', 'agents/', 'commands/', 'hooks/', 'tests/', 'scripts/', 'eslint-rules/'].some(p => file.startsWith(p)) ||
+      ['bin/', 'src/', 'gsd-core/', 'agents/', 'commands/', 'hooks/', 'skills/', 'tests/', 'scripts/', 'eslint-rules/'].some(p => file.startsWith(p)) ||
       file === 'package.json' || file === 'package-lock.json' ||
       (file.startsWith('tsconfig') && file.endsWith('.json')) ||
       file.startsWith('.github/rulesets/')
diff --git a/scripts/gen-golden-install-parity-zcode.cjs b/scripts/gen-golden-install-parity-zcode.cjs
index d755bc251..24e629133 100644
--- a/scripts/gen-golden-install-parity-zcode.cjs
+++ b/scripts/gen-golden-install-parity-zcode.cjs
@@ -15,6 +15,7 @@
  */
 const fs = require('node:fs');
 const path = require('node:path');
+const { execFileSync } = require('node:child_process');
 
 const ROOT = path.resolve(__dirname, '..');
 // buildParityManifest (and its exclusion constants) is the canonical single
@@ -22,7 +23,7 @@ const ROOT = path.resolve(__dirname, '..');
 // generator no longer keeps its own inline copy, which had drifted from the
 // test harness's copy (missing the realpath/`<HOME>` normalization) and
 // mis-generated the claude-local fixture (#2100).
-const { runMinimalInstall, RUNTIME_META, buildParityManifest } = require(path.join(ROOT, 'tests', 'helpers', 'install-shared.cjs'));
+const { runMinimalInstall, RUNTIME_META, buildParityManifest, BUILD_SCRIPT } = require(path.join(ROOT, 'tests', 'helpers', 'install-shared.cjs'));
 const FIXTURE_DIR = path.join(ROOT, 'tests', 'fixtures', 'golden-install-parity');
 
 function cleanup(root) {
@@ -38,6 +39,12 @@ function cleanup(root) {
 const targets = process.argv.slice(2).length > 0 ? process.argv.slice(2) : Object.keys(RUNTIME_META);
 fs.mkdirSync(FIXTURE_DIR, { recursive: true });
 
+// Build hooks/dist before capturing so fixtures are complete even in a clean
+// checkout (hooks/dist is gitignored + built; DEFECT.HOOKS-DIST-SCOPED-CI). The
+// test harness's before() hook does the same; without it a fresh checkout omits
+// every hooks/* path and this generator silently writes short fixtures.
+execFileSync(process.execPath, [BUILD_SCRIPT], { stdio: 'pipe' });
+
 for (const runtime of targets) {
   if (!Object.prototype.hasOwnProperty.call(RUNTIME_META, runtime)) {
     process.stderr.write(`[gen] unknown runtime '${runtime}' (not in RUNTIME_META) — skipping\n`);
diff --git a/scripts/gen-install-tree-fixtures.cjs b/scripts/gen-install-tree-fixtures.cjs
new file mode 100644
index 000000000..3c00fca97
--- /dev/null
+++ b/scripts/gen-install-tree-fixtures.cjs
@@ -0,0 +1,75 @@
+#!/usr/bin/env node
+'use strict';
+/**
+ * Standalone golden-fixture generator for tests/golden-install-tree (#2267 Phase 2).
+ *
+ * This is a BUILD-TIME generation script — NOT a test run. It imports the
+ * canonical buildInstallTree builder from tests/helpers/install-shared.cjs,
+ * which in turn reuses buildParityManifest's exact exclusion set (issue
+ * #2266) so the file-set fixtures here and the golden-install-parity content
+ * fixtures never diverge on which files they cover. The authoritative test
+ * gate remains `gsd-test run`, never a local `node --test`.
+ *
+ * Usage: node scripts/gen-install-tree-fixtures.cjs [runtime ...]
+ */
+const fs = require('node:fs');
+const path = require('node:path');
+const { execFileSync } = require('node:child_process');
+
+const ROOT = path.resolve(__dirname, '..');
+// buildInstallTree (and the exclusion constants it reuses from
+// buildParityManifest) is the canonical single source of truth in
+// tests/helpers/install-shared.cjs (issue #2266/#2267) — this generator does
+// not keep its own inline copy of the walk/exclusion logic.
+const { runMinimalInstall, RUNTIME_META, buildInstallTree, BUILD_SCRIPT } = require(path.join(ROOT, 'tests', 'helpers', 'install-shared.cjs'));
+const FIXTURE_DIR = path.join(ROOT, 'tests', 'fixtures', 'install-tree');
+
+function cleanup(root) {
+  try { fs.rmSync(root, { recursive: true, force: true }); } catch { /* best effort */ }
+}
+
+// Regenerate the fixture for every runtime in RUNTIME_META. Needed when a
+// SHARED gsd-core payload file (e.g. model-catalog.json, capability-registry)
+// changes content — its path appears in every runtime's manifest, so all
+// fixtures must be recaptured together. Usage:
+//   node scripts/gen-install-tree-fixtures.cjs [runtime ...]
+// With no args, regenerates ALL runtimes. With args, only the named runtimes.
+const targets = process.argv.slice(2).length > 0 ? process.argv.slice(2) : Object.keys(RUNTIME_META);
+fs.mkdirSync(FIXTURE_DIR, { recursive: true });
+
+// Build hooks/dist before capturing so fixtures are complete even in a clean
+// checkout (hooks/dist is gitignored + built; DEFECT.HOOKS-DIST-SCOPED-CI). The
+// test harness's before() hook does the same; without it a fresh checkout omits
+// every hooks/* path and this generator silently writes short fixtures.
+execFileSync(process.execPath, [BUILD_SCRIPT], { stdio: 'pipe' });
+
+for (const runtime of targets) {
+  if (!Object.prototype.hasOwnProperty.call(RUNTIME_META, runtime)) {
+    process.stderr.write(`[gen] unknown runtime '${runtime}' (not in RUNTIME_META) — skipping\n`);
+    continue;
+  }
+  const { configDir, root } = runMinimalInstall({ runtime, scope: 'global' });
+  let actual;
+  try {
+    actual = buildInstallTree(configDir, root);
+  } finally {
+    cleanup(root);
+  }
+  const fixturePath = path.join(FIXTURE_DIR, `${runtime}.json`);
+  fs.writeFileSync(fixturePath, JSON.stringify(actual, null, 2) + '\n', 'utf8');
+  process.stdout.write(`[gen] ${runtime}: wrote ${actual.length} paths -> ${fixturePath}\n`);
+}
+
+// Also regenerate the claude LOCAL legacy-layout fixture (claude-local.json).
+// This layout is distinct from the global install (commands/gsd-*.md +
+// agents/gsd-*.md) and has its own snapshot assertion in the test harness.
+const { configDir: localConfigDir, root: localRoot } = runMinimalInstall({ runtime: 'claude', scope: 'local' });
+let localActual;
+try {
+  localActual = buildInstallTree(localConfigDir, localRoot);
+} finally {
+  cleanup(localRoot);
+}
+const localFixturePath = path.join(FIXTURE_DIR, 'claude-local.json');
+fs.writeFileSync(localFixturePath, JSON.stringify(localActual, null, 2) + '\n', 'utf8');
+process.stdout.write(`[gen] claude-local: wrote ${localActual.length} paths -> ${localFixturePath}\n`);
diff --git a/tests/ci-test-scope.test.cjs b/tests/ci-test-scope.test.cjs
index 6f9db506f..7dea2684f 100644
--- a/tests/ci-test-scope.test.cjs
+++ b/tests/ci-test-scope.test.cjs
@@ -581,6 +581,77 @@ describe('golden-install-parity selection (#1691 drift guard)', () => {
   });
 });
 
+describe('shipped install content (golden-parity drift guard, #2267)', () => {
+  // #2266 regression: hooks/gsd-statusline.js changed installed output but no
+  // RULES entry selected golden-install-parity, so stale golden fixtures merged
+  // to `next` undetected. The installer emits hooks/*, commands/*, agents/*,
+  // skills/*, gsd-core/workflows/*, gsd-core/templates/*, gsd-core/references/*,
+  // gsd-core/bin/shared/*.json, and a handful of shipped scripts/* files — every
+  // one of those paths must additionally select golden-install-parity AND the
+  // install-tree snapshot (union semantics: this rule ADDS to whatever
+  // content-specific rule already matched the path).
+  // One path per prefix the rule handles — every installed-source dir the
+  // installer emits. gsd-core/contexts/ is the regression for the review miss
+  // (a real shipped dir that the initial enumeration omitted).
+  const SHIPPED_PATHS = [
+    'hooks/gsd-statusline.js', // exact #2266 regression
+    'gsd-core/workflows/plan-phase.md',
+    'gsd-core/templates/config.json',
+    'gsd-core/references/ui-brand.md',
+    'gsd-core/contexts/dev.md', // regression: initially omitted from the rule
+    'agents/gsd-planner.md',
+    'commands/gsd/mempalace-capture.md',
+    'skills/gsd-explore/SKILL.md',
+    'gsd-core/bin/shared/model-catalog.json',
+    'scripts/changeset/lint.cjs',
+    'scripts/lib/cli-exit.cjs',
+    'scripts/fix-slash-commands.cjs',            // exact-match allowlist entry
+    'scripts/gen-capability-registry.cjs',       // exact-match allowlist entry
+    'scripts/gen-loop-host-contract.cjs',        // exact-match allowlist entry
+  ];
+
+  for (const file of SHIPPED_PATHS) {
+    test(`${file} selects golden-install-parity + golden-install-tree`, () => {
+      const result = scopeFor([file]);
+      assert.strictEqual(result.code_changed, true,
+        `expected code_changed=true for ${file}, got: ${JSON.stringify(result)}`);
+      assert.ok(
+        result.targeted_tests.includes('tests/golden-install-parity.test.cjs'),
+        `expected golden-install-parity in targeted_tests for ${file}, got: ${JSON.stringify(result.targeted_tests)}`,
+      );
+      assert.ok(
+        result.targeted_tests.includes('tests/golden-install-tree.test.cjs'),
+        `expected golden-install-tree in targeted_tests for ${file}, got: ${JSON.stringify(result.targeted_tests)}`,
+      );
+    });
+  }
+
+  test('docs/ change does NOT select golden-install-parity (negative case)', () => {
+    const result = scopeFor(['docs/usage.md']);
+    assert.strictEqual(result.code_changed, false,
+      `expected code_changed=false for docs-only change, got: ${JSON.stringify(result)}`);
+    assert.ok(
+      !result.targeted_tests.includes('tests/golden-install-parity.test.cjs'),
+      `docs-only change must NOT select golden-install-parity, got: ${JSON.stringify(result.targeted_tests)}`,
+    );
+  });
+
+  test('non-shipped scripts/ file does NOT select golden-install-tree (allowlist is exact)', () => {
+    // The rule allowlists only 3 named scripts + scripts/changeset|lib/. A
+    // sibling script that is code but NOT installed verbatim must NOT pull in
+    // the install-tree snapshot — proving this is not a blanket 'scripts/'
+    // prefix that would re-run the golden on every script edit. Assert on
+    // golden-install-TREE (the rule's dedicated test), not parity: many scripts/
+    // paths legitimately select parity via the installer rule's
+    // path.includes('install') substring.
+    const result = scopeFor(['scripts/build-hooks.js']);
+    assert.ok(
+      !result.targeted_tests.includes('tests/golden-install-tree.test.cjs'),
+      `non-shipped script must NOT select golden-install-tree, got: ${JSON.stringify(result.targeted_tests)}`,
+    );
+  });
+});
+
 describe('code_changed=false implies clean output invariant', () => {
   // Fix 1: when code_changed is false, full_matrix, targeted_tests, windows_tests
   // must ALL be empty/false — even if a docs path coincidentally
diff --git a/tests/fixtures/install-tree/antigravity.json b/tests/fixtures/install-tree/antigravity.json
new file mode 100644
index 000000000..129debac2
--- /dev/null
+++ b/tests/fixtures/install-tree/antigravity.json
@@ -0,0 +1,427 @@
+[
+  ".gsd-profile",
+  ".gsd/defaults.json",
+  "agents/gsd-advisor-researcher.md",
+  "agents/gsd-ai-researcher.md",
+  "agents/gsd-assumptions-analyzer.md",
+  "agents/gsd-code-fixer.md",
+  "agents/gsd-code-reviewer.md",
+  "agents/gsd-codebase-mapper.md",
+  "agents/gsd-debug-session-manager.md",
+  "agents/gsd-debugger.md",
+  "agents/gsd-doc-classifier.md",
+  "agents/gsd-doc-synthesizer.md",
+  "agents/gsd-doc-verifier.md",
+  "agents/gsd-doc-writer.md",
+  "agents/gsd-domain-researcher.md",
+  "agents/gsd-eval-auditor.md",
+  "agents/gsd-eval-planner.md",
+  "agents/gsd-executor.md",
+  "agents/gsd-framework-selector.md",
+  "agents/gsd-integration-checker.md",
+  "agents/gsd-intel-updater.md",
+  "agents/gsd-mempalace-curator.md",
+  "agents/gsd-nyquist-auditor.md",
+  "agents/gsd-pattern-mapper.md",
+  "agents/gsd-phase-researcher.md",
+  "agents/gsd-plan-checker.md",
+  "agents/gsd-planner.md",
+  "agents/gsd-project-researcher.md",
+  "agents/gsd-research-synthesizer.md",
+  "agents/gsd-roadmapper.md",
+  "agents/gsd-security-auditor.md",
+  "agents/gsd-ui-auditor.md",
+  "agents/gsd-ui-checker.md",
+  "agents/gsd-ui-researcher.md",
+  "agents/gsd-user-profiler.md",
+  "agents/gsd-verifier.md",
+  "gsd-core/VERSION",
+  "gsd-core/bin/check-latest-version.cjs",
+  "gsd-core/bin/ensure-runtime-build.cjs",
+  "gsd-core/bin/gsd-tools.cjs",
+  "gsd-core/bin/gsd_run",
+  "gsd-core/bin/shared/config-defaults.manifest.json",
+  "gsd-core/bin/shared/config-schema.manifest.json",
+  "gsd-core/bin/shared/model-catalog.json",
+  "gsd-core/bin/shared/runtime-aliases.manifest.json",
+  "gsd-core/bin/verify-reapply-patches.cjs",
+  "gsd-core/contexts/dev.md",
+  "gsd-core/contexts/research.md",
+  "gsd-core/contexts/review.md",
+  "gsd-core/references/agent-contracts.md",
+  "gsd-core/references/agent-skills-bootstrap.md",
+  "gsd-core/references/ai-evals.md",
+  "gsd-core/references/ai-frameworks.md",
+  "gsd-core/references/api-coverage.md",
+  "gsd-core/references/artifact-types.md",
+  "gsd-core/references/autonomous-smart-discuss.md",
+  "gsd-core/references/checkpoints.md",
+  "gsd-core/references/common-bug-patterns.md",
+  "gsd-core/references/context-budget.md",
+  "gsd-core/references/continuation-format.md",
+  "gsd-core/references/debugger-philosophy.md",
+  "gsd-core/references/decimal-phase-calculation.md",
+  "gsd-core/references/doc-conflict-engine.md",
+  "gsd-core/references/domain-probes.md",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/resolutions.json",
+  "gsd-core/references/edge-probe.md",
+  "gsd-core/references/execute-mvp-tdd.md",
+  "gsd-core/references/execute-phase-between-wave-reset.md",
+  "gsd-core/references/execute-phase-context-guard.md",
+  "gsd-core/references/execute-phase-wave-guard.md",
+  "gsd-core/references/executor-examples.md",
+  "gsd-core/references/few-shot-examples/plan-checker.md",
+  "gsd-core/references/few-shot-examples/verifier.md",
+  "gsd-core/references/gate-prompts.md",
+  "gsd-core/references/gates.md",
+  "gsd-core/references/git-integration.md",
+  "gsd-core/references/git-planning-commit.md",
+  "gsd-core/references/gsd-run-resolver.md",
+  "gsd-core/references/honest-verifier.md",
+  "gsd-core/references/ios-scaffold.md",
+  "gsd-core/references/loop-hook-dispatch.md",
+  "gsd-core/references/mandatory-initial-read.md",
+  "gsd-core/references/model-profile-resolution.md",
+  "gsd-core/references/model-profiles.md",
+  "gsd-core/references/mvp-concepts.md",
+  "gsd-core/references/phase-argument-parsing.md",
+  "gsd-core/references/planner-antipatterns.md",
+  "gsd-core/references/planner-chunked.md",
+  "gsd-core/references/planner-gap-closure.md",
+  "gsd-core/references/planner-graphify-auto-update.md",
+  "gsd-core/references/planner-guidance.md",
+  "gsd-core/references/planner-human-verify-mode.md",
+  "gsd-core/references/planner-interface-context.md",
+  "gsd-core/references/planner-load-graph-context.md",
+  "gsd-core/references/planner-mvp-mode.md",
+  "gsd-core/references/planner-reviews.md",
+  "gsd-core/references/planner-revision.md",
+  "gsd-core/references/planner-source-audit.md",
+  "gsd-core/references/planning-config.md",
+  "gsd-core/references/prohibition-probe-fixtures/01-streak-reminder/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/02-clean-utility/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/03-multi-prohibition/expected.json",
+  "gsd-core/references/prohibition-probe.md",
+  "gsd-core/references/project-skills-discovery.md",
+  "gsd-core/references/questioning.md",
+  "gsd-core/references/research-documentation-lookup.md",
+  "gsd-core/references/research-philosophy.md",
+  "gsd-core/references/research-verification-protocol.md",
+  "gsd-core/references/reviewer-instances.md",
+  "gsd-core/references/revision-loop.md",
+  "gsd-core/references/scout-codebase.md",
+  "gsd-core/references/security-asvs-levels.md",
+  "gsd-core/references/skeleton-template.md",
+  "gsd-core/references/sketch-interactivity.md",
+  "gsd-core/references/sketch-theme-system.md",
+  "gsd-core/references/sketch-tooling.md",
+  "gsd-core/references/sketch-variant-patterns.md",
+  "gsd-core/references/specless-probe-fallback.md",
+  "gsd-core/references/spidr-splitting.md",
+  "gsd-core/references/tdd.md",
+  "gsd-core/references/thinking-models-debug.md",
+  "gsd-core/references/thinking-models-execution.md",
+  "gsd-core/references/thinking-models-planning.md",
+  "gsd-core/references/thinking-models-research.md",
+  "gsd-core/references/thinking-models-verification.md",
+  "gsd-core/references/thinking-partner.md",
+  "gsd-core/references/ui-brand.md",
+  "gsd-core/references/ui-consideration-probe.md",
+  "gsd-core/references/universal-anti-patterns.md",
+  "gsd-core/references/untrusted-input-boundary.md",
+  "gsd-core/references/user-profiling.md",
+  "gsd-core/references/user-story-template.md",
+  "gsd-core/references/verification-overrides.md",
+  "gsd-core/references/verification-patterns.md",
+  "gsd-core/references/verify-mvp-mode.md",
+  "gsd-core/references/workstream-flag.md",
+  "gsd-core/references/worktree-branch-check.md",
+  "gsd-core/references/worktree-path-safety.md",
+  "gsd-core/templates/AI-SPEC.md",
+  "gsd-core/templates/DEBUG.md",
+  "gsd-core/templates/README.md",
+  "gsd-core/templates/SECURITY.md",
+  "gsd-core/templates/UAT.md",
+  "gsd-core/templates/UI-SPEC.md",
+  "gsd-core/templates/VALIDATION.md",
+  "gsd-core/templates/claude-md.md",
+  "gsd-core/templates/codebase/architecture.md",
+  "gsd-core/templates/codebase/concerns.md",
+  "gsd-core/templates/codebase/conventions.md",
+  "gsd-core/templates/codebase/integrations.md",
+  "gsd-core/templates/codebase/stack.md",
+  "gsd-core/templates/codebase/structure.md",
+  "gsd-core/templates/codebase/testing.md",
+  "gsd-core/templates/config.json",
+  "gsd-core/templates/context.md",
+  "gsd-core/templates/continue-here.md",
+  "gsd-core/templates/copilot-instructions.md",
+  "gsd-core/templates/debug-subagent-prompt.md",
+  "gsd-core/templates/dev-preferences.md",
+  "gsd-core/templates/discovery.md",
+  "gsd-core/templates/discussion-log.md",
+  "gsd-core/templates/milestone-archive.md",
+  "gsd-core/templates/milestone.md",
+  "gsd-core/templates/phase-prompt.md",
+  "gsd-core/templates/planner-subagent-prompt.md",
+  "gsd-core/templates/project.md",
+  "gsd-core/templates/requirements.md",
+  "gsd-core/templates/research-project/ARCHITECTURE.md",
+  "gsd-core/templates/research-project/FEATURES.md",
+  "gsd-core/templates/research-project/PITFALLS.md",
+  "gsd-core/templates/research-project/STACK.md",
+  "gsd-core/templates/research-project/SUMMARY.md",
+  "gsd-core/templates/research.md",
+  "gsd-core/templates/retrospective.md",
+  "gsd-core/templates/roadmap.md",
+  "gsd-core/templates/spec.md",
+  "gsd-core/templates/state.md",
+  "gsd-core/templates/summary-complex.md",
+  "gsd-core/templates/summary-minimal.md",
+  "gsd-core/templates/summary-standard.md",
+  "gsd-core/templates/summary.md",
+  "gsd-core/templates/user-profile.md",
+  "gsd-core/templates/user-setup.md",
+  "gsd-core/templates/verification-report.md",
+  "gsd-core/workflows/_runtime-launcher.snippet.sh",
+  "gsd-core/workflows/add-backlog.md",
+  "gsd-core/workflows/add-phase.md",
+  "gsd-core/workflows/add-tests.md",
+  "gsd-core/workflows/add-todo.md",
+  "gsd-core/workflows/ai-integration-phase.md",
+  "gsd-core/workflows/analyze-dependencies.md",
+  "gsd-core/workflows/audit-fix.md",
+  "gsd-core/workflows/audit-milestone.md",
+  "gsd-core/workflows/audit-uat.md",
+  "gsd-core/workflows/autonomous.md",
+  "gsd-core/workflows/check-todos.md",
+  "gsd-core/workflows/cleanup.md",
+  "gsd-core/workflows/code-review-fix.md",
+  "gsd-core/workflows/code-review.md",
+  "gsd-core/workflows/complete-milestone.md",
+  "gsd-core/workflows/debug.md",
+  "gsd-core/workflows/diagnose-issues.md",
+  "gsd-core/workflows/discovery-phase.md",
+  "gsd-core/workflows/discuss-phase-assumptions.md",
+  "gsd-core/workflows/discuss-phase-power.md",
+  "gsd-core/workflows/discuss-phase.md",
+  "gsd-core/workflows/discuss-phase/modes/advisor.md",
+  "gsd-core/workflows/discuss-phase/modes/all.md",
+  "gsd-core/workflows/discuss-phase/modes/analyze.md",
+  "gsd-core/workflows/discuss-phase/modes/auto.md",
+  "gsd-core/workflows/discuss-phase/modes/batch.md",
+  "gsd-core/workflows/discuss-phase/modes/chain.md",
+  "gsd-core/workflows/discuss-phase/modes/default.md",
+  "gsd-core/workflows/discuss-phase/modes/power.md",
+  "gsd-core/workflows/discuss-phase/modes/text.md",
+  "gsd-core/workflows/discuss-phase/templates/checkpoint.json",
+  "gsd-core/workflows/discuss-phase/templates/context.md",
+  "gsd-core/workflows/discuss-phase/templates/discussion-log.md",
+  "gsd-core/workflows/do.md",
+  "gsd-core/workflows/docs-update.md",
+  "gsd-core/workflows/edit-phase.md",
+  "gsd-core/workflows/eval-review.md",
+  "gsd-core/workflows/execute-phase.md",
+  "gsd-core/workflows/execute-phase/steps/codebase-drift-gate.md",
+  "gsd-core/workflows/execute-phase/steps/per-plan-worktree-gate.md",
+  "gsd-core/workflows/execute-phase/steps/post-merge-gate.md",
+  "gsd-core/workflows/execute-phase/steps/regression-gate.md",
+  "gsd-core/workflows/execute-phase/steps/worktree-recovery-policy.md",
+  "gsd-core/workflows/execute-plan.md",
+  "gsd-core/workflows/explore.md",
+  "gsd-core/workflows/extract-learnings.md",
+  "gsd-core/workflows/fast.md",
+  "gsd-core/workflows/forensics.md",
+  "gsd-core/workflows/graduation.md",
+  "gsd-core/workflows/health.md",
+  "gsd-core/workflows/help.md",
+  "gsd-core/workflows/help/modes/brief.md",
+  "gsd-core/workflows/help/modes/default.md",
+  "gsd-core/workflows/help/modes/full.md",
+  "gsd-core/workflows/help/modes/topic.md",
+  "gsd-core/workflows/import.md",
+  "gsd-core/workflows/inbox.md",
+  "gsd-core/workflows/ingest-docs.md",
+  "gsd-core/workflows/insert-phase.md",
+  "gsd-core/workflows/list-phase-assumptions.md",
+  "gsd-core/workflows/list-seeds.md",
+  "gsd-core/workflows/list-workspaces.md",
+  "gsd-core/workflows/manager.md",
+  "gsd-core/workflows/map-codebase.md",
+  "gsd-core/workflows/milestone-summary.md",
+  "gsd-core/workflows/mvp-phase.md",
+  "gsd-core/workflows/new-milestone.md",
+  "gsd-core/workflows/new-project.md",
+  "gsd-core/workflows/new-workspace.md",
+  "gsd-core/workflows/next.md",
+  "gsd-core/workflows/node-repair.md",
+  "gsd-core/workflows/note.md",
+  "gsd-core/workflows/onboard.md",
+  "gsd-core/workflows/pause-work.md",
+  "gsd-core/workflows/plan-milestone-gaps.md",
+  "gsd-core/workflows/plan-phase.md",
+  "gsd-core/workflows/plan-phase/steps/closed-phase-gate.md",
+  "gsd-core/workflows/plan-phase/steps/prd-express-path.md",
+  "gsd-core/workflows/plan-phase/steps/windows-troubleshooting.md",
+  "gsd-core/workflows/plan-review-convergence.md",
+  "gsd-core/workflows/plant-seed.md",
+  "gsd-core/workflows/pr-branch.md",
+  "gsd-core/workflows/profile-user.md",
+  "gsd-core/workflows/progress.md",
+  "gsd-core/workflows/quick.md",
+  "gsd-core/workflows/reapply-patches.md",
+  "gsd-core/workflows/remove-phase.md",
+  "gsd-core/workflows/remove-workspace.md",
+  "gsd-core/workflows/resume-project.md",
+  "gsd-core/workflows/review.md",
+  "gsd-core/workflows/scan.md",
+  "gsd-core/workflows/secure-phase.md",
+  "gsd-core/workflows/session-report.md",
+  "gsd-core/workflows/settings-advanced.md",
+  "gsd-core/workflows/settings-integrations.md",
+  "gsd-core/workflows/settings.md",
+  "gsd-core/workflows/ship.md",
+  "gsd-core/workflows/sketch-wrap-up.md",
+  "gsd-core/workflows/sketch.md",
+  "gsd-core/workflows/smart-entry.md",
+  "gsd-core/workflows/spec-phase.md",
+  "gsd-core/workflows/spike-wrap-up.md",
+  "gsd-core/workflows/spike.md",
+  "gsd-core/workflows/stats.md",
+  "gsd-core/workflows/sync-skills.md",
+  "gsd-core/workflows/thread.md",
+  "gsd-core/workflows/transition.md",
+  "gsd-core/workflows/ui-phase.md",
+  "gsd-core/workflows/ui-review.md",
+  "gsd-core/workflows/ultraplan-phase.md",
+  "gsd-core/workflows/undo.md",
+  "gsd-core/workflows/update.md",
+  "gsd-core/workflows/validate-phase.md",
+  "gsd-core/workflows/verify-phase.md",
+  "gsd-core/workflows/verify-work.md",
+  "hooks/gsd-check-update-worker.js",
+  "hooks/gsd-check-update.js",
+  "hooks/gsd-config-reload.js",
+  "hooks/gsd-context-monitor.js",
+  "hooks/gsd-cursor-post-tool.js",
+  "hooks/gsd-cursor-pre-tool.js",
+  "hooks/gsd-cursor-session-start.js",
+  "hooks/gsd-cursor-stop.js",
+  "hooks/gsd-cursor-subagent-start.js",
+  "hooks/gsd-cursor-subagent-stop.js",
+  "hooks/gsd-ensure-canonical-path.js",
+  "hooks/gsd-graphify-update.sh",
+  "hooks/gsd-phase-boundary.sh",
+  "hooks/gsd-prompt-guard.js",
+  "hooks/gsd-read-guard.js",
+  "hooks/gsd-read-injection-scanner.js",
+  "hooks/gsd-session-state.sh",
+  "hooks/gsd-statusline.js",
+  "hooks/gsd-update-banner.js",
+  "hooks/gsd-validate-commit.sh",
+  "hooks/gsd-windsurf-pre-command.js",
+  "hooks/gsd-windsurf-pre-write.js",
+  "hooks/gsd-workflow-guard.js",
+  "hooks/gsd-worktree-path-guard.js",
+  "hooks/lib/git-cmd.js",
+  "hooks/lib/gsd-graphify-rebuild.sh",
+  "hooks/managed-hooks-registry.cjs",
+  "mcp_config.json",
+  "package.json",
+  "scripts/changeset/README.md",
+  "scripts/changeset/cli.cjs",
+  "scripts/changeset/github-release-notes.cjs",
+  "scripts/changeset/lint.cjs",
+  "scripts/changeset/new.cjs",
+  "scripts/changeset/parse.cjs",
+  "scripts/changeset/render.cjs",
+  "scripts/changeset/serialize.cjs",
+  "scripts/fix-slash-commands.cjs",
+  "scripts/gen-capability-registry.cjs",
+  "scripts/gen-loop-host-contract.cjs",
+  "scripts/lib/allowlist-ratchet.cjs",
+  "scripts/lib/cli-exit.cjs",
+  "skills/gsd-add-tests/SKILL.md",
+  "skills/gsd-ai-integration-phase/SKILL.md",
+  "skills/gsd-audit-fix/SKILL.md",
+  "skills/gsd-audit-milestone/SKILL.md",
+  "skills/gsd-audit-uat/SKILL.md",
+  "skills/gsd-autonomous/SKILL.md",
+  "skills/gsd-capture/SKILL.md",
+  "skills/gsd-cleanup/SKILL.md",
+  "skills/gsd-code-review/SKILL.md",
+  "skills/gsd-complete-milestone/SKILL.md",
+  "skills/gsd-config/SKILL.md",
+  "skills/gsd-debug/SKILL.md",
+  "skills/gsd-discuss-phase/SKILL.md",
+  "skills/gsd-docs-update/SKILL.md",
+  "skills/gsd-eval-review/SKILL.md",
+  "skills/gsd-execute-phase/SKILL.md",
+  "skills/gsd-explore/SKILL.md",
+  "skills/gsd-extract-learnings/SKILL.md",
+  "skills/gsd-fast/SKILL.md",
+  "skills/gsd-forensics/SKILL.md",
+  "skills/gsd-graphify/SKILL.md",
+  "skills/gsd-health/SKILL.md",
+  "skills/gsd-help/SKILL.md",
+  "skills/gsd-import/SKILL.md",
+  "skills/gsd-inbox/SKILL.md",
+  "skills/gsd-ingest-docs/SKILL.md",
+  "skills/gsd-manager/SKILL.md",
+  "skills/gsd-map-codebase/SKILL.md",
+  "skills/gsd-mempalace-capture/SKILL.md",
+  "skills/gsd-mempalace-recall/SKILL.md",
+  "skills/gsd-milestone-summary/SKILL.md",
+  "skills/gsd-mvp-phase/SKILL.md",
+  "skills/gsd-new-milestone/SKILL.md",
+  "skills/gsd-new-project/SKILL.md",
+  "skills/gsd-next/SKILL.md",
+  "skills/gsd-ns-context/SKILL.md",
+  "skills/gsd-ns-ideate/SKILL.md",
+  "skills/gsd-ns-manage/SKILL.md",
+  "skills/gsd-ns-project/SKILL.md",
+  "skills/gsd-ns-review/SKILL.md",
+  "skills/gsd-ns-workflow/SKILL.md",
+  "skills/gsd-onboard/SKILL.md",
+  "skills/gsd-pause-work/SKILL.md",
+  "skills/gsd-phase/SKILL.md",
+  "skills/gsd-plan-phase/SKILL.md",
+  "skills/gsd-plan-review-convergence/SKILL.md",
+  "skills/gsd-pr-branch/SKILL.md",
+  "skills/gsd-profile-user/SKILL.md",
+  "skills/gsd-progress/SKILL.md",
+  "skills/gsd-quick/SKILL.md",
+  "skills/gsd-resume-work/SKILL.md",
+  "skills/gsd-review-backlog/SKILL.md",
+  "skills/gsd-review/SKILL.md",
+  "skills/gsd-secure-phase/SKILL.md",
+  "skills/gsd-settings/SKILL.md",
+  "skills/gsd-ship/SKILL.md",
+  "skills/gsd-sketch/SKILL.md",
+  "skills/gsd-spec-phase/SKILL.md",
+  "skills/gsd-spike/SKILL.md",
+  "skills/gsd-stats/SKILL.md",
+  "skills/gsd-surface/SKILL.md",
+  "skills/gsd-thread/SKILL.md",
+  "skills/gsd-ui-phase/SKILL.md",
+  "skills/gsd-ui-review/SKILL.md",
+  "skills/gsd-ultraplan-phase/SKILL.md",
+  "skills/gsd-undo/SKILL.md",
+  "skills/gsd-update/SKILL.md",
+  "skills/gsd-validate-phase/SKILL.md",
+  "skills/gsd-verify-work/SKILL.md",
+  "skills/gsd-workspace/SKILL.md",
+  "skills/gsd-workstreams/SKILL.md"
+]
diff --git a/tests/fixtures/install-tree/augment.json b/tests/fixtures/install-tree/augment.json
new file mode 100644
index 000000000..1c5977a7c
--- /dev/null
+++ b/tests/fixtures/install-tree/augment.json
@@ -0,0 +1,498 @@
+[
+  ".gsd-profile",
+  ".gsd/defaults.json",
+  "agents/gsd-advisor-researcher.md",
+  "agents/gsd-ai-researcher.md",
+  "agents/gsd-assumptions-analyzer.md",
+  "agents/gsd-code-fixer.md",
+  "agents/gsd-code-reviewer.md",
+  "agents/gsd-codebase-mapper.md",
+  "agents/gsd-debug-session-manager.md",
+  "agents/gsd-debugger.md",
+  "agents/gsd-doc-classifier.md",
+  "agents/gsd-doc-synthesizer.md",
+  "agents/gsd-doc-verifier.md",
+  "agents/gsd-doc-writer.md",
+  "agents/gsd-domain-researcher.md",
+  "agents/gsd-eval-auditor.md",
+  "agents/gsd-eval-planner.md",
+  "agents/gsd-executor.md",
+  "agents/gsd-framework-selector.md",
+  "agents/gsd-integration-checker.md",
+  "agents/gsd-intel-updater.md",
+  "agents/gsd-mempalace-curator.md",
+  "agents/gsd-nyquist-auditor.md",
+  "agents/gsd-pattern-mapper.md",
+  "agents/gsd-phase-researcher.md",
+  "agents/gsd-plan-checker.md",
+  "agents/gsd-planner.md",
+  "agents/gsd-project-researcher.md",
+  "agents/gsd-research-synthesizer.md",
+  "agents/gsd-roadmapper.md",
+  "agents/gsd-security-auditor.md",
+  "agents/gsd-ui-auditor.md",
+  "agents/gsd-ui-checker.md",
+  "agents/gsd-ui-researcher.md",
+  "agents/gsd-user-profiler.md",
+  "agents/gsd-verifier.md",
+  "commands/gsd-add-tests.md",
+  "commands/gsd-ai-integration-phase.md",
+  "commands/gsd-audit-fix.md",
+  "commands/gsd-audit-milestone.md",
+  "commands/gsd-audit-uat.md",
+  "commands/gsd-autonomous.md",
+  "commands/gsd-capture.md",
+  "commands/gsd-cleanup.md",
+  "commands/gsd-code-review.md",
+  "commands/gsd-complete-milestone.md",
+  "commands/gsd-config.md",
+  "commands/gsd-debug.md",
+  "commands/gsd-discuss-phase.md",
+  "commands/gsd-docs-update.md",
+  "commands/gsd-eval-review.md",
+  "commands/gsd-execute-phase.md",
+  "commands/gsd-explore.md",
+  "commands/gsd-extract-learnings.md",
+  "commands/gsd-fast.md",
+  "commands/gsd-forensics.md",
+  "commands/gsd-graphify.md",
+  "commands/gsd-health.md",
+  "commands/gsd-help.md",
+  "commands/gsd-import.md",
+  "commands/gsd-inbox.md",
+  "commands/gsd-ingest-docs.md",
+  "commands/gsd-manager.md",
+  "commands/gsd-map-codebase.md",
+  "commands/gsd-mempalace-capture.md",
+  "commands/gsd-mempalace-recall.md",
+  "commands/gsd-milestone-summary.md",
+  "commands/gsd-mvp-phase.md",
+  "commands/gsd-new-milestone.md",
+  "commands/gsd-new-project.md",
+  "commands/gsd-next.md",
+  "commands/gsd-ns-context.md",
+  "commands/gsd-ns-ideate.md",
+  "commands/gsd-ns-manage.md",
+  "commands/gsd-ns-project.md",
+  "commands/gsd-ns-review.md",
+  "commands/gsd-ns-workflow.md",
+  "commands/gsd-onboard.md",
+  "commands/gsd-pause-work.md",
+  "commands/gsd-phase.md",
+  "commands/gsd-plan-phase.md",
+  "commands/gsd-plan-review-convergence.md",
+  "commands/gsd-pr-branch.md",
+  "commands/gsd-profile-user.md",
+  "commands/gsd-progress.md",
+  "commands/gsd-quick.md",
+  "commands/gsd-resume-work.md",
+  "commands/gsd-review-backlog.md",
+  "commands/gsd-review.md",
+  "commands/gsd-secure-phase.md",
+  "commands/gsd-settings.md",
+  "commands/gsd-ship.md",
+  "commands/gsd-sketch.md",
+  "commands/gsd-spec-phase.md",
+  "commands/gsd-spike.md",
+  "commands/gsd-stats.md",
+  "commands/gsd-surface.md",
+  "commands/gsd-thread.md",
+  "commands/gsd-ui-phase.md",
+  "commands/gsd-ui-review.md",
+  "commands/gsd-ultraplan-phase.md",
+  "commands/gsd-undo.md",
+  "commands/gsd-update.md",
+  "commands/gsd-validate-phase.md",
+  "commands/gsd-verify-work.md",
+  "commands/gsd-workspace.md",
+  "commands/gsd-workstreams.md",
+  "gsd-core/VERSION",
+  "gsd-core/bin/check-latest-version.cjs",
+  "gsd-core/bin/ensure-runtime-build.cjs",
+  "gsd-core/bin/gsd-tools.cjs",
+  "gsd-core/bin/gsd_run",
+  "gsd-core/bin/shared/config-defaults.manifest.json",
+  "gsd-core/bin/shared/config-schema.manifest.json",
+  "gsd-core/bin/shared/model-catalog.json",
+  "gsd-core/bin/shared/runtime-aliases.manifest.json",
+  "gsd-core/bin/verify-reapply-patches.cjs",
+  "gsd-core/contexts/dev.md",
+  "gsd-core/contexts/research.md",
+  "gsd-core/contexts/review.md",
+  "gsd-core/references/agent-contracts.md",
+  "gsd-core/references/agent-skills-bootstrap.md",
+  "gsd-core/references/ai-evals.md",
+  "gsd-core/references/ai-frameworks.md",
+  "gsd-core/references/api-coverage.md",
+  "gsd-core/references/artifact-types.md",
+  "gsd-core/references/autonomous-smart-discuss.md",
+  "gsd-core/references/checkpoints.md",
+  "gsd-core/references/common-bug-patterns.md",
+  "gsd-core/references/context-budget.md",
+  "gsd-core/references/continuation-format.md",
+  "gsd-core/references/debugger-philosophy.md",
+  "gsd-core/references/decimal-phase-calculation.md",
+  "gsd-core/references/doc-conflict-engine.md",
+  "gsd-core/references/domain-probes.md",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/resolutions.json",
+  "gsd-core/references/edge-probe.md",
+  "gsd-core/references/execute-mvp-tdd.md",
+  "gsd-core/references/execute-phase-between-wave-reset.md",
+  "gsd-core/references/execute-phase-context-guard.md",
+  "gsd-core/references/execute-phase-wave-guard.md",
+  "gsd-core/references/executor-examples.md",
+  "gsd-core/references/few-shot-examples/plan-checker.md",
+  "gsd-core/references/few-shot-examples/verifier.md",
+  "gsd-core/references/gate-prompts.md",
+  "gsd-core/references/gates.md",
+  "gsd-core/references/git-integration.md",
+  "gsd-core/references/git-planning-commit.md",
+  "gsd-core/references/gsd-run-resolver.md",
+  "gsd-core/references/honest-verifier.md",
+  "gsd-core/references/ios-scaffold.md",
+  "gsd-core/references/loop-hook-dispatch.md",
+  "gsd-core/references/mandatory-initial-read.md",
+  "gsd-core/references/model-profile-resolution.md",
+  "gsd-core/references/model-profiles.md",
+  "gsd-core/references/mvp-concepts.md",
+  "gsd-core/references/phase-argument-parsing.md",
+  "gsd-core/references/planner-antipatterns.md",
+  "gsd-core/references/planner-chunked.md",
+  "gsd-core/references/planner-gap-closure.md",
+  "gsd-core/references/planner-graphify-auto-update.md",
+  "gsd-core/references/planner-guidance.md",
+  "gsd-core/references/planner-human-verify-mode.md",
+  "gsd-core/references/planner-interface-context.md",
+  "gsd-core/references/planner-load-graph-context.md",
+  "gsd-core/references/planner-mvp-mode.md",
+  "gsd-core/references/planner-reviews.md",
+  "gsd-core/references/planner-revision.md",
+  "gsd-core/references/planner-source-audit.md",
+  "gsd-core/references/planning-config.md",
+  "gsd-core/references/prohibition-probe-fixtures/01-streak-reminder/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/02-clean-utility/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/03-multi-prohibition/expected.json",
+  "gsd-core/references/prohibition-probe.md",
+  "gsd-core/references/project-skills-discovery.md",
+  "gsd-core/references/questioning.md",
+  "gsd-core/references/research-documentation-lookup.md",
+  "gsd-core/references/research-philosophy.md",
+  "gsd-core/references/research-verification-protocol.md",
+  "gsd-core/references/reviewer-instances.md",
+  "gsd-core/references/revision-loop.md",
+  "gsd-core/references/scout-codebase.md",
+  "gsd-core/references/security-asvs-levels.md",
+  "gsd-core/references/skeleton-template.md",
+  "gsd-core/references/sketch-interactivity.md",
+  "gsd-core/references/sketch-theme-system.md",
+  "gsd-core/references/sketch-tooling.md",
+  "gsd-core/references/sketch-variant-patterns.md",
+  "gsd-core/references/specless-probe-fallback.md",
+  "gsd-core/references/spidr-splitting.md",
+  "gsd-core/references/tdd.md",
+  "gsd-core/references/thinking-models-debug.md",
+  "gsd-core/references/thinking-models-execution.md",
+  "gsd-core/references/thinking-models-planning.md",
+  "gsd-core/references/thinking-models-research.md",
+  "gsd-core/references/thinking-models-verification.md",
+  "gsd-core/references/thinking-partner.md",
+  "gsd-core/references/ui-brand.md",
+  "gsd-core/references/ui-consideration-probe.md",
+  "gsd-core/references/universal-anti-patterns.md",
+  "gsd-core/references/untrusted-input-boundary.md",
+  "gsd-core/references/user-profiling.md",
+  "gsd-core/references/user-story-template.md",
+  "gsd-core/references/verification-overrides.md",
+  "gsd-core/references/verification-patterns.md",
+  "gsd-core/references/verify-mvp-mode.md",
+  "gsd-core/references/workstream-flag.md",
+  "gsd-core/references/worktree-branch-check.md",
+  "gsd-core/references/worktree-path-safety.md",
+  "gsd-core/templates/AI-SPEC.md",
+  "gsd-core/templates/DEBUG.md",
+  "gsd-core/templates/README.md",
+  "gsd-core/templates/SECURITY.md",
+  "gsd-core/templates/UAT.md",
+  "gsd-core/templates/UI-SPEC.md",
+  "gsd-core/templates/VALIDATION.md",
+  "gsd-core/templates/claude-md.md",
+  "gsd-core/templates/codebase/architecture.md",
+  "gsd-core/templates/codebase/concerns.md",
+  "gsd-core/templates/codebase/conventions.md",
+  "gsd-core/templates/codebase/integrations.md",
+  "gsd-core/templates/codebase/stack.md",
+  "gsd-core/templates/codebase/structure.md",
+  "gsd-core/templates/codebase/testing.md",
+  "gsd-core/templates/config.json",
+  "gsd-core/templates/context.md",
+  "gsd-core/templates/continue-here.md",
+  "gsd-core/templates/copilot-instructions.md",
+  "gsd-core/templates/debug-subagent-prompt.md",
+  "gsd-core/templates/dev-preferences.md",
+  "gsd-core/templates/discovery.md",
+  "gsd-core/templates/discussion-log.md",
+  "gsd-core/templates/milestone-archive.md",
+  "gsd-core/templates/milestone.md",
+  "gsd-core/templates/phase-prompt.md",
+  "gsd-core/templates/planner-subagent-prompt.md",
+  "gsd-core/templates/project.md",
+  "gsd-core/templates/requirements.md",
+  "gsd-core/templates/research-project/ARCHITECTURE.md",
+  "gsd-core/templates/research-project/FEATURES.md",
+  "gsd-core/templates/research-project/PITFALLS.md",
+  "gsd-core/templates/research-project/STACK.md",
+  "gsd-core/templates/research-project/SUMMARY.md",
+  "gsd-core/templates/research.md",
+  "gsd-core/templates/retrospective.md",
+  "gsd-core/templates/roadmap.md",
+  "gsd-core/templates/spec.md",
+  "gsd-core/templates/state.md",
+  "gsd-core/templates/summary-complex.md",
+  "gsd-core/templates/summary-minimal.md",
+  "gsd-core/templates/summary-standard.md",
+  "gsd-core/templates/summary.md",
+  "gsd-core/templates/user-profile.md",
+  "gsd-core/templates/user-setup.md",
+  "gsd-core/templates/verification-report.md",
+  "gsd-core/workflows/_runtime-launcher.snippet.sh",
+  "gsd-core/workflows/add-backlog.md",
+  "gsd-core/workflows/add-phase.md",
+  "gsd-core/workflows/add-tests.md",
+  "gsd-core/workflows/add-todo.md",
+  "gsd-core/workflows/ai-integration-phase.md",
+  "gsd-core/workflows/analyze-dependencies.md",
+  "gsd-core/workflows/audit-fix.md",
+  "gsd-core/workflows/audit-milestone.md",
+  "gsd-core/workflows/audit-uat.md",
+  "gsd-core/workflows/autonomous.md",
+  "gsd-core/workflows/check-todos.md",
+  "gsd-core/workflows/cleanup.md",
+  "gsd-core/workflows/code-review-fix.md",
+  "gsd-core/workflows/code-review.md",
+  "gsd-core/workflows/complete-milestone.md",
+  "gsd-core/workflows/debug.md",
+  "gsd-core/workflows/diagnose-issues.md",
+  "gsd-core/workflows/discovery-phase.md",
+  "gsd-core/workflows/discuss-phase-assumptions.md",
+  "gsd-core/workflows/discuss-phase-power.md",
+  "gsd-core/workflows/discuss-phase.md",
+  "gsd-core/workflows/discuss-phase/modes/advisor.md",
+  "gsd-core/workflows/discuss-phase/modes/all.md",
+  "gsd-core/workflows/discuss-phase/modes/analyze.md",
+  "gsd-core/workflows/discuss-phase/modes/auto.md",
+  "gsd-core/workflows/discuss-phase/modes/batch.md",
+  "gsd-core/workflows/discuss-phase/modes/chain.md",
+  "gsd-core/workflows/discuss-phase/modes/default.md",
+  "gsd-core/workflows/discuss-phase/modes/power.md",
+  "gsd-core/workflows/discuss-phase/modes/text.md",
+  "gsd-core/workflows/discuss-phase/templates/checkpoint.json",
+  "gsd-core/workflows/discuss-phase/templates/context.md",
+  "gsd-core/workflows/discuss-phase/templates/discussion-log.md",
+  "gsd-core/workflows/do.md",
+  "gsd-core/workflows/docs-update.md",
+  "gsd-core/workflows/edit-phase.md",
+  "gsd-core/workflows/eval-review.md",
+  "gsd-core/workflows/execute-phase.md",
+  "gsd-core/workflows/execute-phase/steps/codebase-drift-gate.md",
+  "gsd-core/workflows/execute-phase/steps/per-plan-worktree-gate.md",
+  "gsd-core/workflows/execute-phase/steps/post-merge-gate.md",
+  "gsd-core/workflows/execute-phase/steps/regression-gate.md",
+  "gsd-core/workflows/execute-phase/steps/worktree-recovery-policy.md",
+  "gsd-core/workflows/execute-plan.md",
+  "gsd-core/workflows/explore.md",
+  "gsd-core/workflows/extract-learnings.md",
+  "gsd-core/workflows/fast.md",
+  "gsd-core/workflows/forensics.md",
+  "gsd-core/workflows/graduation.md",
+  "gsd-core/workflows/health.md",
+  "gsd-core/workflows/help.md",
+  "gsd-core/workflows/help/modes/brief.md",
+  "gsd-core/workflows/help/modes/default.md",
+  "gsd-core/workflows/help/modes/full.md",
+  "gsd-core/workflows/help/modes/topic.md",
+  "gsd-core/workflows/import.md",
+  "gsd-core/workflows/inbox.md",
+  "gsd-core/workflows/ingest-docs.md",
+  "gsd-core/workflows/insert-phase.md",
+  "gsd-core/workflows/list-phase-assumptions.md",
+  "gsd-core/workflows/list-seeds.md",
+  "gsd-core/workflows/list-workspaces.md",
+  "gsd-core/workflows/manager.md",
+  "gsd-core/workflows/map-codebase.md",
+  "gsd-core/workflows/milestone-summary.md",
+  "gsd-core/workflows/mvp-phase.md",
+  "gsd-core/workflows/new-milestone.md",
+  "gsd-core/workflows/new-project.md",
+  "gsd-core/workflows/new-workspace.md",
+  "gsd-core/workflows/next.md",
+  "gsd-core/workflows/node-repair.md",
+  "gsd-core/workflows/note.md",
+  "gsd-core/workflows/onboard.md",
+  "gsd-core/workflows/pause-work.md",
+  "gsd-core/workflows/plan-milestone-gaps.md",
+  "gsd-core/workflows/plan-phase.md",
+  "gsd-core/workflows/plan-phase/steps/closed-phase-gate.md",
+  "gsd-core/workflows/plan-phase/steps/prd-express-path.md",
+  "gsd-core/workflows/plan-phase/steps/windows-troubleshooting.md",
+  "gsd-core/workflows/plan-review-convergence.md",
+  "gsd-core/workflows/plant-seed.md",
+  "gsd-core/workflows/pr-branch.md",
+  "gsd-core/workflows/profile-user.md",
+  "gsd-core/workflows/progress.md",
+  "gsd-core/workflows/quick.md",
+  "gsd-core/workflows/reapply-patches.md",
+  "gsd-core/workflows/remove-phase.md",
+  "gsd-core/workflows/remove-workspace.md",
+  "gsd-core/workflows/resume-project.md",
+  "gsd-core/workflows/review.md",
+  "gsd-core/workflows/scan.md",
+  "gsd-core/workflows/secure-phase.md",
+  "gsd-core/workflows/session-report.md",
+  "gsd-core/workflows/settings-advanced.md",
+  "gsd-core/workflows/settings-integrations.md",
+  "gsd-core/workflows/settings.md",
+  "gsd-core/workflows/ship.md",
+  "gsd-core/workflows/sketch-wrap-up.md",
+  "gsd-core/workflows/sketch.md",
+  "gsd-core/workflows/smart-entry.md",
+  "gsd-core/workflows/spec-phase.md",
+  "gsd-core/workflows/spike-wrap-up.md",
+  "gsd-core/workflows/spike.md",
+  "gsd-core/workflows/stats.md",
+  "gsd-core/workflows/sync-skills.md",
+  "gsd-core/workflows/thread.md",
+  "gsd-core/workflows/transition.md",
+  "gsd-core/workflows/ui-phase.md",
+  "gsd-core/workflows/ui-review.md",
+  "gsd-core/workflows/ultraplan-phase.md",
+  "gsd-core/workflows/undo.md",
+  "gsd-core/workflows/update.md",
+  "gsd-core/workflows/validate-phase.md",
+  "gsd-core/workflows/verify-phase.md",
+  "gsd-core/workflows/verify-work.md",
+  "hooks/gsd-check-update-worker.js",
+  "hooks/gsd-check-update.js",
+  "hooks/gsd-config-reload.js",
+  "hooks/gsd-context-monitor.js",
+  "hooks/gsd-cursor-post-tool.js",
+  "hooks/gsd-cursor-pre-tool.js",
+  "hooks/gsd-cursor-session-start.js",
+  "hooks/gsd-cursor-stop.js",
+  "hooks/gsd-cursor-subagent-start.js",
+  "hooks/gsd-cursor-subagent-stop.js",
+  "hooks/gsd-ensure-canonical-path.js",
+  "hooks/gsd-graphify-update.sh",
+  "hooks/gsd-phase-boundary.sh",
+  "hooks/gsd-prompt-guard.js",
+  "hooks/gsd-read-guard.js",
+  "hooks/gsd-read-injection-scanner.js",
+  "hooks/gsd-session-state.sh",
+  "hooks/gsd-statusline.js",
+  "hooks/gsd-update-banner.js",
+  "hooks/gsd-validate-commit.sh",
+  "hooks/gsd-windsurf-pre-command.js",
+  "hooks/gsd-windsurf-pre-write.js",
+  "hooks/gsd-workflow-guard.js",
+  "hooks/gsd-worktree-path-guard.js",
+  "hooks/lib/git-cmd.js",
+  "hooks/lib/gsd-graphify-rebuild.sh",
+  "hooks/managed-hooks-registry.cjs",
+  "package.json",
+  "scripts/changeset/README.md",
+  "scripts/changeset/cli.cjs",
+  "scripts/changeset/github-release-notes.cjs",
+  "scripts/changeset/lint.cjs",
+  "scripts/changeset/new.cjs",
+  "scripts/changeset/parse.cjs",
+  "scripts/changeset/render.cjs",
+  "scripts/changeset/serialize.cjs",
+  "scripts/fix-slash-commands.cjs",
+  "scripts/gen-capability-registry.cjs",
+  "scripts/gen-loop-host-contract.cjs",
+  "scripts/lib/allowlist-ratchet.cjs",
+  "scripts/lib/cli-exit.cjs",
+  "skills/gsd-ns-context/SKILL.md",
+  "skills/gsd-ns-context/skills/docs-update/SKILL.md",
+  "skills/gsd-ns-context/skills/extract-learnings/SKILL.md",
+  "skills/gsd-ns-context/skills/graphify/SKILL.md",
+  "skills/gsd-ns-context/skills/map-codebase/SKILL.md",
+  "skills/gsd-ns-context/skills/mempalace-capture/SKILL.md",
+  "skills/gsd-ns-context/skills/mempalace-recall/SKILL.md",
+  "skills/gsd-ns-ideate/SKILL.md",
+  "skills/gsd-ns-ideate/skills/capture/SKILL.md",
+  "skills/gsd-ns-ideate/skills/explore/SKILL.md",
+  "skills/gsd-ns-ideate/skills/sketch/SKILL.md",
+  "skills/gsd-ns-ideate/skills/spec-phase/SKILL.md",
+  "skills/gsd-ns-ideate/skills/spike/SKILL.md",
+  "skills/gsd-ns-manage/SKILL.md",
+  "skills/gsd-ns-manage/skills/cleanup/SKILL.md",
+  "skills/gsd-ns-manage/skills/config/SKILL.md",
+  "skills/gsd-ns-manage/skills/health/SKILL.md",
+  "skills/gsd-ns-manage/skills/help/SKILL.md",
+  "skills/gsd-ns-manage/skills/inbox/SKILL.md",
+  "skills/gsd-ns-manage/skills/manager/SKILL.md",
+  "skills/gsd-ns-manage/skills/pause-work/SKILL.md",
+  "skills/gsd-ns-manage/skills/pr-branch/SKILL.md",
+  "skills/gsd-ns-manage/skills/resume-work/SKILL.md",
+  "skills/gsd-ns-manage/skills/settings/SKILL.md",
+  "skills/gsd-ns-manage/skills/ship/SKILL.md",
+  "skills/gsd-ns-manage/skills/stats/SKILL.md",
+  "skills/gsd-ns-manage/skills/surface/SKILL.md",
+  "skills/gsd-ns-manage/skills/thread/SKILL.md",
+  "skills/gsd-ns-manage/skills/undo/SKILL.md",
+  "skills/gsd-ns-manage/skills/update/SKILL.md",
+  "skills/gsd-ns-manage/skills/workspace/SKILL.md",
+  "skills/gsd-ns-manage/skills/workstreams/SKILL.md",
+  "skills/gsd-ns-project/SKILL.md",
+  "skills/gsd-ns-project/skills/audit-milestone/SKILL.md",
+  "skills/gsd-ns-project/skills/complete-milestone/SKILL.md",
+  "skills/gsd-ns-project/skills/import/SKILL.md",
+  "skills/gsd-ns-project/skills/ingest-docs/SKILL.md",
+  "skills/gsd-ns-project/skills/milestone-summary/SKILL.md",
+  "skills/gsd-ns-project/skills/new-milestone/SKILL.md",
+  "skills/gsd-ns-project/skills/new-project/SKILL.md",
+  "skills/gsd-ns-project/skills/onboard/SKILL.md",
+  "skills/gsd-ns-project/skills/profile-user/SKILL.md",
+  "skills/gsd-ns-project/skills/review-backlog/SKILL.md",
+  "skills/gsd-ns-review/SKILL.md",
+  "skills/gsd-ns-review/skills/audit-fix/SKILL.md",
+  "skills/gsd-ns-review/skills/audit-uat/SKILL.md",
+  "skills/gsd-ns-review/skills/code-review/SKILL.md",
+  "skills/gsd-ns-review/skills/debug/SKILL.md",
+  "skills/gsd-ns-review/skills/eval-review/SKILL.md",
+  "skills/gsd-ns-review/skills/forensics/SKILL.md",
+  "skills/gsd-ns-review/skills/review/SKILL.md",
+  "skills/gsd-ns-review/skills/secure-phase/SKILL.md",
+  "skills/gsd-ns-review/skills/ui-phase/SKILL.md",
+  "skills/gsd-ns-review/skills/ui-review/SKILL.md",
+  "skills/gsd-ns-review/skills/validate-phase/SKILL.md",
+  "skills/gsd-ns-workflow/SKILL.md",
+  "skills/gsd-ns-workflow/skills/add-tests/SKILL.md",
+  "skills/gsd-ns-workflow/skills/ai-integration-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/autonomous/SKILL.md",
+  "skills/gsd-ns-workflow/skills/discuss-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/execute-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/fast/SKILL.md",
+  "skills/gsd-ns-workflow/skills/mvp-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/next/SKILL.md",
+  "skills/gsd-ns-workflow/skills/phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/plan-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/plan-review-convergence/SKILL.md",
+  "skills/gsd-ns-workflow/skills/progress/SKILL.md",
+  "skills/gsd-ns-workflow/skills/quick/SKILL.md",
+  "skills/gsd-ns-workflow/skills/spec-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/ultraplan-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/verify-work/SKILL.md"
+]
diff --git a/tests/fixtures/install-tree/claude-local.json b/tests/fixtures/install-tree/claude-local.json
new file mode 100644
index 000000000..46d4776ea
--- /dev/null
+++ b/tests/fixtures/install-tree/claude-local.json
@@ -0,0 +1,425 @@
+[
+  ".gsd-profile",
+  "agents/gsd-advisor-researcher.md",
+  "agents/gsd-ai-researcher.md",
+  "agents/gsd-assumptions-analyzer.md",
+  "agents/gsd-code-fixer.md",
+  "agents/gsd-code-reviewer.md",
+  "agents/gsd-codebase-mapper.md",
+  "agents/gsd-debug-session-manager.md",
+  "agents/gsd-debugger.md",
+  "agents/gsd-doc-classifier.md",
+  "agents/gsd-doc-synthesizer.md",
+  "agents/gsd-doc-verifier.md",
+  "agents/gsd-doc-writer.md",
+  "agents/gsd-domain-researcher.md",
+  "agents/gsd-eval-auditor.md",
+  "agents/gsd-eval-planner.md",
+  "agents/gsd-executor.md",
+  "agents/gsd-framework-selector.md",
+  "agents/gsd-integration-checker.md",
+  "agents/gsd-intel-updater.md",
+  "agents/gsd-mempalace-curator.md",
+  "agents/gsd-nyquist-auditor.md",
+  "agents/gsd-pattern-mapper.md",
+  "agents/gsd-phase-researcher.md",
+  "agents/gsd-plan-checker.md",
+  "agents/gsd-planner.md",
+  "agents/gsd-project-researcher.md",
+  "agents/gsd-research-synthesizer.md",
+  "agents/gsd-roadmapper.md",
+  "agents/gsd-security-auditor.md",
+  "agents/gsd-ui-auditor.md",
+  "agents/gsd-ui-checker.md",
+  "agents/gsd-ui-researcher.md",
+  "agents/gsd-user-profiler.md",
+  "agents/gsd-verifier.md",
+  "commands/gsd-add-tests.md",
+  "commands/gsd-ai-integration-phase.md",
+  "commands/gsd-audit-fix.md",
+  "commands/gsd-audit-milestone.md",
+  "commands/gsd-audit-uat.md",
+  "commands/gsd-autonomous.md",
+  "commands/gsd-capture.md",
+  "commands/gsd-cleanup.md",
+  "commands/gsd-code-review.md",
+  "commands/gsd-complete-milestone.md",
+  "commands/gsd-config.md",
+  "commands/gsd-debug.md",
+  "commands/gsd-discuss-phase.md",
+  "commands/gsd-docs-update.md",
+  "commands/gsd-eval-review.md",
+  "commands/gsd-execute-phase.md",
+  "commands/gsd-explore.md",
+  "commands/gsd-extract-learnings.md",
+  "commands/gsd-fast.md",
+  "commands/gsd-forensics.md",
+  "commands/gsd-graphify.md",
+  "commands/gsd-health.md",
+  "commands/gsd-help.md",
+  "commands/gsd-import.md",
+  "commands/gsd-inbox.md",
+  "commands/gsd-ingest-docs.md",
+  "commands/gsd-manager.md",
+  "commands/gsd-map-codebase.md",
+  "commands/gsd-mempalace-capture.md",
+  "commands/gsd-mempalace-recall.md",
+  "commands/gsd-milestone-summary.md",
+  "commands/gsd-mvp-phase.md",
+  "commands/gsd-new-milestone.md",
+  "commands/gsd-new-project.md",
+  "commands/gsd-next.md",
+  "commands/gsd-ns-context.md",
+  "commands/gsd-ns-ideate.md",
+  "commands/gsd-ns-manage.md",
+  "commands/gsd-ns-project.md",
+  "commands/gsd-ns-review.md",
+  "commands/gsd-ns-workflow.md",
+  "commands/gsd-onboard.md",
+  "commands/gsd-pause-work.md",
+  "commands/gsd-phase.md",
+  "commands/gsd-plan-phase.md",
+  "commands/gsd-plan-review-convergence.md",
+  "commands/gsd-pr-branch.md",
+  "commands/gsd-profile-user.md",
+  "commands/gsd-progress.md",
+  "commands/gsd-quick.md",
+  "commands/gsd-resume-work.md",
+  "commands/gsd-review-backlog.md",
+  "commands/gsd-review.md",
+  "commands/gsd-secure-phase.md",
+  "commands/gsd-settings.md",
+  "commands/gsd-ship.md",
+  "commands/gsd-sketch.md",
+  "commands/gsd-spec-phase.md",
+  "commands/gsd-spike.md",
+  "commands/gsd-stats.md",
+  "commands/gsd-surface.md",
+  "commands/gsd-thread.md",
+  "commands/gsd-ui-phase.md",
+  "commands/gsd-ui-review.md",
+  "commands/gsd-ultraplan-phase.md",
+  "commands/gsd-undo.md",
+  "commands/gsd-update.md",
+  "commands/gsd-validate-phase.md",
+  "commands/gsd-verify-work.md",
+  "commands/gsd-workspace.md",
+  "commands/gsd-workstreams.md",
+  "gsd-core/VERSION",
+  "gsd-core/bin/check-latest-version.cjs",
+  "gsd-core/bin/ensure-runtime-build.cjs",
+  "gsd-core/bin/gsd-tools.cjs",
+  "gsd-core/bin/gsd_run",
+  "gsd-core/bin/shared/config-defaults.manifest.json",
+  "gsd-core/bin/shared/config-schema.manifest.json",
+  "gsd-core/bin/shared/model-catalog.json",
+  "gsd-core/bin/shared/runtime-aliases.manifest.json",
+  "gsd-core/bin/verify-reapply-patches.cjs",
+  "gsd-core/contexts/dev.md",
+  "gsd-core/contexts/research.md",
+  "gsd-core/contexts/review.md",
+  "gsd-core/references/agent-contracts.md",
+  "gsd-core/references/agent-skills-bootstrap.md",
+  "gsd-core/references/ai-evals.md",
+  "gsd-core/references/ai-frameworks.md",
+  "gsd-core/references/api-coverage.md",
+  "gsd-core/references/artifact-types.md",
+  "gsd-core/references/autonomous-smart-discuss.md",
+  "gsd-core/references/checkpoints.md",
+  "gsd-core/references/common-bug-patterns.md",
+  "gsd-core/references/context-budget.md",
+  "gsd-core/references/continuation-format.md",
+  "gsd-core/references/debugger-philosophy.md",
+  "gsd-core/references/decimal-phase-calculation.md",
+  "gsd-core/references/doc-conflict-engine.md",
+  "gsd-core/references/domain-probes.md",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/resolutions.json",
+  "gsd-core/references/edge-probe.md",
+  "gsd-core/references/execute-mvp-tdd.md",
+  "gsd-core/references/execute-phase-between-wave-reset.md",
+  "gsd-core/references/execute-phase-context-guard.md",
+  "gsd-core/references/execute-phase-wave-guard.md",
+  "gsd-core/references/executor-examples.md",
+  "gsd-core/references/few-shot-examples/plan-checker.md",
+  "gsd-core/references/few-shot-examples/verifier.md",
+  "gsd-core/references/gate-prompts.md",
+  "gsd-core/references/gates.md",
+  "gsd-core/references/git-integration.md",
+  "gsd-core/references/git-planning-commit.md",
+  "gsd-core/references/gsd-run-resolver.md",
+  "gsd-core/references/honest-verifier.md",
+  "gsd-core/references/ios-scaffold.md",
+  "gsd-core/references/loop-hook-dispatch.md",
+  "gsd-core/references/mandatory-initial-read.md",
+  "gsd-core/references/model-profile-resolution.md",
+  "gsd-core/references/model-profiles.md",
+  "gsd-core/references/mvp-concepts.md",
+  "gsd-core/references/phase-argument-parsing.md",
+  "gsd-core/references/planner-antipatterns.md",
+  "gsd-core/references/planner-chunked.md",
+  "gsd-core/references/planner-gap-closure.md",
+  "gsd-core/references/planner-graphify-auto-update.md",
+  "gsd-core/references/planner-guidance.md",
+  "gsd-core/references/planner-human-verify-mode.md",
+  "gsd-core/references/planner-interface-context.md",
+  "gsd-core/references/planner-load-graph-context.md",
+  "gsd-core/references/planner-mvp-mode.md",
+  "gsd-core/references/planner-reviews.md",
+  "gsd-core/references/planner-revision.md",
+  "gsd-core/references/planner-source-audit.md",
+  "gsd-core/references/planning-config.md",
+  "gsd-core/references/prohibition-probe-fixtures/01-streak-reminder/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/02-clean-utility/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/03-multi-prohibition/expected.json",
+  "gsd-core/references/prohibition-probe.md",
+  "gsd-core/references/project-skills-discovery.md",
+  "gsd-core/references/questioning.md",
+  "gsd-core/references/research-documentation-lookup.md",
+  "gsd-core/references/research-philosophy.md",
+  "gsd-core/references/research-verification-protocol.md",
+  "gsd-core/references/reviewer-instances.md",
+  "gsd-core/references/revision-loop.md",
+  "gsd-core/references/scout-codebase.md",
+  "gsd-core/references/security-asvs-levels.md",
+  "gsd-core/references/skeleton-template.md",
+  "gsd-core/references/sketch-interactivity.md",
+  "gsd-core/references/sketch-theme-system.md",
+  "gsd-core/references/sketch-tooling.md",
+  "gsd-core/references/sketch-variant-patterns.md",
+  "gsd-core/references/specless-probe-fallback.md",
+  "gsd-core/references/spidr-splitting.md",
+  "gsd-core/references/tdd.md",
+  "gsd-core/references/thinking-models-debug.md",
+  "gsd-core/references/thinking-models-execution.md",
+  "gsd-core/references/thinking-models-planning.md",
+  "gsd-core/references/thinking-models-research.md",
+  "gsd-core/references/thinking-models-verification.md",
+  "gsd-core/references/thinking-partner.md",
+  "gsd-core/references/ui-brand.md",
+  "gsd-core/references/ui-consideration-probe.md",
+  "gsd-core/references/universal-anti-patterns.md",
+  "gsd-core/references/untrusted-input-boundary.md",
+  "gsd-core/references/user-profiling.md",
+  "gsd-core/references/user-story-template.md",
+  "gsd-core/references/verification-overrides.md",
+  "gsd-core/references/verification-patterns.md",
+  "gsd-core/references/verify-mvp-mode.md",
+  "gsd-core/references/workstream-flag.md",
+  "gsd-core/references/worktree-branch-check.md",
+  "gsd-core/references/worktree-path-safety.md",
+  "gsd-core/templates/AI-SPEC.md",
+  "gsd-core/templates/DEBUG.md",
+  "gsd-core/templates/README.md",
+  "gsd-core/templates/SECURITY.md",
+  "gsd-core/templates/UAT.md",
+  "gsd-core/templates/UI-SPEC.md",
+  "gsd-core/templates/VALIDATION.md",
+  "gsd-core/templates/claude-md.md",
+  "gsd-core/templates/codebase/architecture.md",
+  "gsd-core/templates/codebase/concerns.md",
+  "gsd-core/templates/codebase/conventions.md",
+  "gsd-core/templates/codebase/integrations.md",
+  "gsd-core/templates/codebase/stack.md",
+  "gsd-core/templates/codebase/structure.md",
+  "gsd-core/templates/codebase/testing.md",
+  "gsd-core/templates/config.json",
+  "gsd-core/templates/context.md",
+  "gsd-core/templates/continue-here.md",
+  "gsd-core/templates/copilot-instructions.md",
+  "gsd-core/templates/debug-subagent-prompt.md",
+  "gsd-core/templates/dev-preferences.md",
+  "gsd-core/templates/discovery.md",
+  "gsd-core/templates/discussion-log.md",
+  "gsd-core/templates/milestone-archive.md",
+  "gsd-core/templates/milestone.md",
+  "gsd-core/templates/phase-prompt.md",
+  "gsd-core/templates/planner-subagent-prompt.md",
+  "gsd-core/templates/project.md",
+  "gsd-core/templates/requirements.md",
+  "gsd-core/templates/research-project/ARCHITECTURE.md",
+  "gsd-core/templates/research-project/FEATURES.md",
+  "gsd-core/templates/research-project/PITFALLS.md",
+  "gsd-core/templates/research-project/STACK.md",
+  "gsd-core/templates/research-project/SUMMARY.md",
+  "gsd-core/templates/research.md",
+  "gsd-core/templates/retrospective.md",
+  "gsd-core/templates/roadmap.md",
+  "gsd-core/templates/spec.md",
+  "gsd-core/templates/state.md",
+  "gsd-core/templates/summary-complex.md",
+  "gsd-core/templates/summary-minimal.md",
+  "gsd-core/templates/summary-standard.md",
+  "gsd-core/templates/summary.md",
+  "gsd-core/templates/user-profile.md",
+  "gsd-core/templates/user-setup.md",
+  "gsd-core/templates/verification-report.md",
+  "gsd-core/workflows/_runtime-launcher.snippet.sh",
+  "gsd-core/workflows/add-backlog.md",
+  "gsd-core/workflows/add-phase.md",
+  "gsd-core/workflows/add-tests.md",
+  "gsd-core/workflows/add-todo.md",
+  "gsd-core/workflows/ai-integration-phase.md",
+  "gsd-core/workflows/analyze-dependencies.md",
+  "gsd-core/workflows/audit-fix.md",
+  "gsd-core/workflows/audit-milestone.md",
+  "gsd-core/workflows/audit-uat.md",
+  "gsd-core/workflows/autonomous.md",
+  "gsd-core/workflows/check-todos.md",
+  "gsd-core/workflows/cleanup.md",
+  "gsd-core/workflows/code-review-fix.md",
+  "gsd-core/workflows/code-review.md",
+  "gsd-core/workflows/complete-milestone.md",
+  "gsd-core/workflows/debug.md",
+  "gsd-core/workflows/diagnose-issues.md",
+  "gsd-core/workflows/discovery-phase.md",
+  "gsd-core/workflows/discuss-phase-assumptions.md",
+  "gsd-core/workflows/discuss-phase-power.md",
+  "gsd-core/workflows/discuss-phase.md",
+  "gsd-core/workflows/discuss-phase/modes/advisor.md",
+  "gsd-core/workflows/discuss-phase/modes/all.md",
+  "gsd-core/workflows/discuss-phase/modes/analyze.md",
+  "gsd-core/workflows/discuss-phase/modes/auto.md",
+  "gsd-core/workflows/discuss-phase/modes/batch.md",
+  "gsd-core/workflows/discuss-phase/modes/chain.md",
+  "gsd-core/workflows/discuss-phase/modes/default.md",
+  "gsd-core/workflows/discuss-phase/modes/power.md",
+  "gsd-core/workflows/discuss-phase/modes/text.md",
+  "gsd-core/workflows/discuss-phase/templates/checkpoint.json",
+  "gsd-core/workflows/discuss-phase/templates/context.md",
+  "gsd-core/workflows/discuss-phase/templates/discussion-log.md",
+  "gsd-core/workflows/do.md",
+  "gsd-core/workflows/docs-update.md",
+  "gsd-core/workflows/edit-phase.md",
+  "gsd-core/workflows/eval-review.md",
+  "gsd-core/workflows/execute-phase.md",
+  "gsd-core/workflows/execute-phase/steps/codebase-drift-gate.md",
+  "gsd-core/workflows/execute-phase/steps/per-plan-worktree-gate.md",
+  "gsd-core/workflows/execute-phase/steps/post-merge-gate.md",
+  "gsd-core/workflows/execute-phase/steps/regression-gate.md",
+  "gsd-core/workflows/execute-phase/steps/worktree-recovery-policy.md",
+  "gsd-core/workflows/execute-plan.md",
+  "gsd-core/workflows/explore.md",
+  "gsd-core/workflows/extract-learnings.md",
+  "gsd-core/workflows/fast.md",
+  "gsd-core/workflows/forensics.md",
+  "gsd-core/workflows/graduation.md",
+  "gsd-core/workflows/health.md",
+  "gsd-core/workflows/help.md",
+  "gsd-core/workflows/help/modes/brief.md",
+  "gsd-core/workflows/help/modes/default.md",
+  "gsd-core/workflows/help/modes/full.md",
+  "gsd-core/workflows/help/modes/topic.md",
+  "gsd-core/workflows/import.md",
+  "gsd-core/workflows/inbox.md",
+  "gsd-core/workflows/ingest-docs.md",
+  "gsd-core/workflows/insert-phase.md",
+  "gsd-core/workflows/list-phase-assumptions.md",
+  "gsd-core/workflows/list-seeds.md",
+  "gsd-core/workflows/list-workspaces.md",
+  "gsd-core/workflows/manager.md",
+  "gsd-core/workflows/map-codebase.md",
+  "gsd-core/workflows/milestone-summary.md",
+  "gsd-core/workflows/mvp-phase.md",
+  "gsd-core/workflows/new-milestone.md",
+  "gsd-core/workflows/new-project.md",
+  "gsd-core/workflows/new-workspace.md",
+  "gsd-core/workflows/next.md",
+  "gsd-core/workflows/node-repair.md",
+  "gsd-core/workflows/note.md",
+  "gsd-core/workflows/onboard.md",
+  "gsd-core/workflows/pause-work.md",
+  "gsd-core/workflows/plan-milestone-gaps.md",
+  "gsd-core/workflows/plan-phase.md",
+  "gsd-core/workflows/plan-phase/steps/closed-phase-gate.md",
+  "gsd-core/workflows/plan-phase/steps/prd-express-path.md",
+  "gsd-core/workflows/plan-phase/steps/windows-troubleshooting.md",
+  "gsd-core/workflows/plan-review-convergence.md",
+  "gsd-core/workflows/plant-seed.md",
+  "gsd-core/workflows/pr-branch.md",
+  "gsd-core/workflows/profile-user.md",
+  "gsd-core/workflows/progress.md",
+  "gsd-core/workflows/quick.md",
+  "gsd-core/workflows/reapply-patches.md",
+  "gsd-core/workflows/remove-phase.md",
+  "gsd-core/workflows/remove-workspace.md",
+  "gsd-core/workflows/resume-project.md",
+  "gsd-core/workflows/review.md",
+  "gsd-core/workflows/scan.md",
+  "gsd-core/workflows/secure-phase.md",
+  "gsd-core/workflows/session-report.md",
+  "gsd-core/workflows/settings-advanced.md",
+  "gsd-core/workflows/settings-integrations.md",
+  "gsd-core/workflows/settings.md",
+  "gsd-core/workflows/ship.md",
+  "gsd-core/workflows/sketch-wrap-up.md",
+  "gsd-core/workflows/sketch.md",
+  "gsd-core/workflows/smart-entry.md",
+  "gsd-core/workflows/spec-phase.md",
+  "gsd-core/workflows/spike-wrap-up.md",
+  "gsd-core/workflows/spike.md",
+  "gsd-core/workflows/stats.md",
+  "gsd-core/workflows/sync-skills.md",
+  "gsd-core/workflows/thread.md",
+  "gsd-core/workflows/transition.md",
+  "gsd-core/workflows/ui-phase.md",
+  "gsd-core/workflows/ui-review.md",
+  "gsd-core/workflows/ultraplan-phase.md",
+  "gsd-core/workflows/undo.md",
+  "gsd-core/workflows/update.md",
+  "gsd-core/workflows/validate-phase.md",
+  "gsd-core/workflows/verify-phase.md",
+  "gsd-core/workflows/verify-work.md",
+  "hooks/gsd-check-update-worker.js",
+  "hooks/gsd-check-update.js",
+  "hooks/gsd-config-reload.js",
+  "hooks/gsd-context-monitor.js",
+  "hooks/gsd-cursor-post-tool.js",
+  "hooks/gsd-cursor-pre-tool.js",
+  "hooks/gsd-cursor-session-start.js",
+  "hooks/gsd-cursor-stop.js",
+  "hooks/gsd-cursor-subagent-start.js",
+  "hooks/gsd-cursor-subagent-stop.js",
+  "hooks/gsd-ensure-canonical-path.js",
+  "hooks/gsd-graphify-update.sh",
+  "hooks/gsd-phase-boundary.sh",
+  "hooks/gsd-prompt-guard.js",
+  "hooks/gsd-read-guard.js",
+  "hooks/gsd-read-injection-scanner.js",
+  "hooks/gsd-session-state.sh",
+  "hooks/gsd-statusline.js",
+  "hooks/gsd-update-banner.js",
+  "hooks/gsd-validate-commit.sh",
+  "hooks/gsd-windsurf-pre-command.js",
+  "hooks/gsd-windsurf-pre-write.js",
+  "hooks/gsd-workflow-guard.js",
+  "hooks/gsd-worktree-path-guard.js",
+  "hooks/lib/git-cmd.js",
+  "hooks/lib/gsd-graphify-rebuild.sh",
+  "hooks/managed-hooks-registry.cjs",
+  "package.json",
+  "scripts/changeset/README.md",
+  "scripts/changeset/cli.cjs",
+  "scripts/changeset/github-release-notes.cjs",
+  "scripts/changeset/lint.cjs",
+  "scripts/changeset/new.cjs",
+  "scripts/changeset/parse.cjs",
+  "scripts/changeset/render.cjs",
+  "scripts/changeset/serialize.cjs",
+  "scripts/fix-slash-commands.cjs",
+  "scripts/gen-capability-registry.cjs",
+  "scripts/gen-loop-host-contract.cjs",
+  "scripts/lib/allowlist-ratchet.cjs",
+  "scripts/lib/cli-exit.cjs"
+]
diff --git a/tests/fixtures/install-tree/claude.json b/tests/fixtures/install-tree/claude.json
new file mode 100644
index 000000000..656bf934b
--- /dev/null
+++ b/tests/fixtures/install-tree/claude.json
@@ -0,0 +1,425 @@
+[
+  ".gsd-profile",
+  "agents/gsd-advisor-researcher.md",
+  "agents/gsd-ai-researcher.md",
+  "agents/gsd-assumptions-analyzer.md",
+  "agents/gsd-code-fixer.md",
+  "agents/gsd-code-reviewer.md",
+  "agents/gsd-codebase-mapper.md",
+  "agents/gsd-debug-session-manager.md",
+  "agents/gsd-debugger.md",
+  "agents/gsd-doc-classifier.md",
+  "agents/gsd-doc-synthesizer.md",
+  "agents/gsd-doc-verifier.md",
+  "agents/gsd-doc-writer.md",
+  "agents/gsd-domain-researcher.md",
+  "agents/gsd-eval-auditor.md",
+  "agents/gsd-eval-planner.md",
+  "agents/gsd-executor.md",
+  "agents/gsd-framework-selector.md",
+  "agents/gsd-integration-checker.md",
+  "agents/gsd-intel-updater.md",
+  "agents/gsd-mempalace-curator.md",
+  "agents/gsd-nyquist-auditor.md",
+  "agents/gsd-pattern-mapper.md",
+  "agents/gsd-phase-researcher.md",
+  "agents/gsd-plan-checker.md",
+  "agents/gsd-planner.md",
+  "agents/gsd-project-researcher.md",
+  "agents/gsd-research-synthesizer.md",
+  "agents/gsd-roadmapper.md",
+  "agents/gsd-security-auditor.md",
+  "agents/gsd-ui-auditor.md",
+  "agents/gsd-ui-checker.md",
+  "agents/gsd-ui-researcher.md",
+  "agents/gsd-user-profiler.md",
+  "agents/gsd-verifier.md",
+  "gsd-core/VERSION",
+  "gsd-core/bin/check-latest-version.cjs",
+  "gsd-core/bin/ensure-runtime-build.cjs",
+  "gsd-core/bin/gsd-tools.cjs",
+  "gsd-core/bin/gsd_run",
+  "gsd-core/bin/shared/config-defaults.manifest.json",
+  "gsd-core/bin/shared/config-schema.manifest.json",
+  "gsd-core/bin/shared/model-catalog.json",
+  "gsd-core/bin/shared/runtime-aliases.manifest.json",
+  "gsd-core/bin/verify-reapply-patches.cjs",
+  "gsd-core/contexts/dev.md",
+  "gsd-core/contexts/research.md",
+  "gsd-core/contexts/review.md",
+  "gsd-core/references/agent-contracts.md",
+  "gsd-core/references/agent-skills-bootstrap.md",
+  "gsd-core/references/ai-evals.md",
+  "gsd-core/references/ai-frameworks.md",
+  "gsd-core/references/api-coverage.md",
+  "gsd-core/references/artifact-types.md",
+  "gsd-core/references/autonomous-smart-discuss.md",
+  "gsd-core/references/checkpoints.md",
+  "gsd-core/references/common-bug-patterns.md",
+  "gsd-core/references/context-budget.md",
+  "gsd-core/references/continuation-format.md",
+  "gsd-core/references/debugger-philosophy.md",
+  "gsd-core/references/decimal-phase-calculation.md",
+  "gsd-core/references/doc-conflict-engine.md",
+  "gsd-core/references/domain-probes.md",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/resolutions.json",
+  "gsd-core/references/edge-probe.md",
+  "gsd-core/references/execute-mvp-tdd.md",
+  "gsd-core/references/execute-phase-between-wave-reset.md",
+  "gsd-core/references/execute-phase-context-guard.md",
+  "gsd-core/references/execute-phase-wave-guard.md",
+  "gsd-core/references/executor-examples.md",
+  "gsd-core/references/few-shot-examples/plan-checker.md",
+  "gsd-core/references/few-shot-examples/verifier.md",
+  "gsd-core/references/gate-prompts.md",
+  "gsd-core/references/gates.md",
+  "gsd-core/references/git-integration.md",
+  "gsd-core/references/git-planning-commit.md",
+  "gsd-core/references/gsd-run-resolver.md",
+  "gsd-core/references/honest-verifier.md",
+  "gsd-core/references/ios-scaffold.md",
+  "gsd-core/references/loop-hook-dispatch.md",
+  "gsd-core/references/mandatory-initial-read.md",
+  "gsd-core/references/model-profile-resolution.md",
+  "gsd-core/references/model-profiles.md",
+  "gsd-core/references/mvp-concepts.md",
+  "gsd-core/references/phase-argument-parsing.md",
+  "gsd-core/references/planner-antipatterns.md",
+  "gsd-core/references/planner-chunked.md",
+  "gsd-core/references/planner-gap-closure.md",
+  "gsd-core/references/planner-graphify-auto-update.md",
+  "gsd-core/references/planner-guidance.md",
+  "gsd-core/references/planner-human-verify-mode.md",
+  "gsd-core/references/planner-interface-context.md",
+  "gsd-core/references/planner-load-graph-context.md",
+  "gsd-core/references/planner-mvp-mode.md",
+  "gsd-core/references/planner-reviews.md",
+  "gsd-core/references/planner-revision.md",
+  "gsd-core/references/planner-source-audit.md",
+  "gsd-core/references/planning-config.md",
+  "gsd-core/references/prohibition-probe-fixtures/01-streak-reminder/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/02-clean-utility/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/03-multi-prohibition/expected.json",
+  "gsd-core/references/prohibition-probe.md",
+  "gsd-core/references/project-skills-discovery.md",
+  "gsd-core/references/questioning.md",
+  "gsd-core/references/research-documentation-lookup.md",
+  "gsd-core/references/research-philosophy.md",
+  "gsd-core/references/research-verification-protocol.md",
+  "gsd-core/references/reviewer-instances.md",
+  "gsd-core/references/revision-loop.md",
+  "gsd-core/references/scout-codebase.md",
+  "gsd-core/references/security-asvs-levels.md",
+  "gsd-core/references/skeleton-template.md",
+  "gsd-core/references/sketch-interactivity.md",
+  "gsd-core/references/sketch-theme-system.md",
+  "gsd-core/references/sketch-tooling.md",
+  "gsd-core/references/sketch-variant-patterns.md",
+  "gsd-core/references/specless-probe-fallback.md",
+  "gsd-core/references/spidr-splitting.md",
+  "gsd-core/references/tdd.md",
+  "gsd-core/references/thinking-models-debug.md",
+  "gsd-core/references/thinking-models-execution.md",
+  "gsd-core/references/thinking-models-planning.md",
+  "gsd-core/references/thinking-models-research.md",
+  "gsd-core/references/thinking-models-verification.md",
+  "gsd-core/references/thinking-partner.md",
+  "gsd-core/references/ui-brand.md",
+  "gsd-core/references/ui-consideration-probe.md",
+  "gsd-core/references/universal-anti-patterns.md",
+  "gsd-core/references/untrusted-input-boundary.md",
+  "gsd-core/references/user-profiling.md",
+  "gsd-core/references/user-story-template.md",
+  "gsd-core/references/verification-overrides.md",
+  "gsd-core/references/verification-patterns.md",
+  "gsd-core/references/verify-mvp-mode.md",
+  "gsd-core/references/workstream-flag.md",
+  "gsd-core/references/worktree-branch-check.md",
+  "gsd-core/references/worktree-path-safety.md",
+  "gsd-core/templates/AI-SPEC.md",
+  "gsd-core/templates/DEBUG.md",
+  "gsd-core/templates/README.md",
+  "gsd-core/templates/SECURITY.md",
+  "gsd-core/templates/UAT.md",
+  "gsd-core/templates/UI-SPEC.md",
+  "gsd-core/templates/VALIDATION.md",
+  "gsd-core/templates/claude-md.md",
+  "gsd-core/templates/codebase/architecture.md",
+  "gsd-core/templates/codebase/concerns.md",
+  "gsd-core/templates/codebase/conventions.md",
+  "gsd-core/templates/codebase/integrations.md",
+  "gsd-core/templates/codebase/stack.md",
+  "gsd-core/templates/codebase/structure.md",
+  "gsd-core/templates/codebase/testing.md",
+  "gsd-core/templates/config.json",
+  "gsd-core/templates/context.md",
+  "gsd-core/templates/continue-here.md",
+  "gsd-core/templates/copilot-instructions.md",
+  "gsd-core/templates/debug-subagent-prompt.md",
+  "gsd-core/templates/dev-preferences.md",
+  "gsd-core/templates/discovery.md",
+  "gsd-core/templates/discussion-log.md",
+  "gsd-core/templates/milestone-archive.md",
+  "gsd-core/templates/milestone.md",
+  "gsd-core/templates/phase-prompt.md",
+  "gsd-core/templates/planner-subagent-prompt.md",
+  "gsd-core/templates/project.md",
+  "gsd-core/templates/requirements.md",
+  "gsd-core/templates/research-project/ARCHITECTURE.md",
+  "gsd-core/templates/research-project/FEATURES.md",
+  "gsd-core/templates/research-project/PITFALLS.md",
+  "gsd-core/templates/research-project/STACK.md",
+  "gsd-core/templates/research-project/SUMMARY.md",
+  "gsd-core/templates/research.md",
+  "gsd-core/templates/retrospective.md",
+  "gsd-core/templates/roadmap.md",
+  "gsd-core/templates/spec.md",
+  "gsd-core/templates/state.md",
+  "gsd-core/templates/summary-complex.md",
+  "gsd-core/templates/summary-minimal.md",
+  "gsd-core/templates/summary-standard.md",
+  "gsd-core/templates/summary.md",
+  "gsd-core/templates/user-profile.md",
+  "gsd-core/templates/user-setup.md",
+  "gsd-core/templates/verification-report.md",
+  "gsd-core/workflows/_runtime-launcher.snippet.sh",
+  "gsd-core/workflows/add-backlog.md",
+  "gsd-core/workflows/add-phase.md",
+  "gsd-core/workflows/add-tests.md",
+  "gsd-core/workflows/add-todo.md",
+  "gsd-core/workflows/ai-integration-phase.md",
+  "gsd-core/workflows/analyze-dependencies.md",
+  "gsd-core/workflows/audit-fix.md",
+  "gsd-core/workflows/audit-milestone.md",
+  "gsd-core/workflows/audit-uat.md",
+  "gsd-core/workflows/autonomous.md",
+  "gsd-core/workflows/check-todos.md",
+  "gsd-core/workflows/cleanup.md",
+  "gsd-core/workflows/code-review-fix.md",
+  "gsd-core/workflows/code-review.md",
+  "gsd-core/workflows/complete-milestone.md",
+  "gsd-core/workflows/debug.md",
+  "gsd-core/workflows/diagnose-issues.md",
+  "gsd-core/workflows/discovery-phase.md",
+  "gsd-core/workflows/discuss-phase-assumptions.md",
+  "gsd-core/workflows/discuss-phase-power.md",
+  "gsd-core/workflows/discuss-phase.md",
+  "gsd-core/workflows/discuss-phase/modes/advisor.md",
+  "gsd-core/workflows/discuss-phase/modes/all.md",
+  "gsd-core/workflows/discuss-phase/modes/analyze.md",
+  "gsd-core/workflows/discuss-phase/modes/auto.md",
+  "gsd-core/workflows/discuss-phase/modes/batch.md",
+  "gsd-core/workflows/discuss-phase/modes/chain.md",
+  "gsd-core/workflows/discuss-phase/modes/default.md",
+  "gsd-core/workflows/discuss-phase/modes/power.md",
+  "gsd-core/workflows/discuss-phase/modes/text.md",
+  "gsd-core/workflows/discuss-phase/templates/checkpoint.json",
+  "gsd-core/workflows/discuss-phase/templates/context.md",
+  "gsd-core/workflows/discuss-phase/templates/discussion-log.md",
+  "gsd-core/workflows/do.md",
+  "gsd-core/workflows/docs-update.md",
+  "gsd-core/workflows/edit-phase.md",
+  "gsd-core/workflows/eval-review.md",
+  "gsd-core/workflows/execute-phase.md",
+  "gsd-core/workflows/execute-phase/steps/codebase-drift-gate.md",
+  "gsd-core/workflows/execute-phase/steps/per-plan-worktree-gate.md",
+  "gsd-core/workflows/execute-phase/steps/post-merge-gate.md",
+  "gsd-core/workflows/execute-phase/steps/regression-gate.md",
+  "gsd-core/workflows/execute-phase/steps/worktree-recovery-policy.md",
+  "gsd-core/workflows/execute-plan.md",
+  "gsd-core/workflows/explore.md",
+  "gsd-core/workflows/extract-learnings.md",
+  "gsd-core/workflows/fast.md",
+  "gsd-core/workflows/forensics.md",
+  "gsd-core/workflows/graduation.md",
+  "gsd-core/workflows/health.md",
+  "gsd-core/workflows/help.md",
+  "gsd-core/workflows/help/modes/brief.md",
+  "gsd-core/workflows/help/modes/default.md",
+  "gsd-core/workflows/help/modes/full.md",
+  "gsd-core/workflows/help/modes/topic.md",
+  "gsd-core/workflows/import.md",
+  "gsd-core/workflows/inbox.md",
+  "gsd-core/workflows/ingest-docs.md",
+  "gsd-core/workflows/insert-phase.md",
+  "gsd-core/workflows/list-phase-assumptions.md",
+  "gsd-core/workflows/list-seeds.md",
+  "gsd-core/workflows/list-workspaces.md",
+  "gsd-core/workflows/manager.md",
+  "gsd-core/workflows/map-codebase.md",
+  "gsd-core/workflows/milestone-summary.md",
+  "gsd-core/workflows/mvp-phase.md",
+  "gsd-core/workflows/new-milestone.md",
+  "gsd-core/workflows/new-project.md",
+  "gsd-core/workflows/new-workspace.md",
+  "gsd-core/workflows/next.md",
+  "gsd-core/workflows/node-repair.md",
+  "gsd-core/workflows/note.md",
+  "gsd-core/workflows/onboard.md",
+  "gsd-core/workflows/pause-work.md",
+  "gsd-core/workflows/plan-milestone-gaps.md",
+  "gsd-core/workflows/plan-phase.md",
+  "gsd-core/workflows/plan-phase/steps/closed-phase-gate.md",
+  "gsd-core/workflows/plan-phase/steps/prd-express-path.md",
+  "gsd-core/workflows/plan-phase/steps/windows-troubleshooting.md",
+  "gsd-core/workflows/plan-review-convergence.md",
+  "gsd-core/workflows/plant-seed.md",
+  "gsd-core/workflows/pr-branch.md",
+  "gsd-core/workflows/profile-user.md",
+  "gsd-core/workflows/progress.md",
+  "gsd-core/workflows/quick.md",
+  "gsd-core/workflows/reapply-patches.md",
+  "gsd-core/workflows/remove-phase.md",
+  "gsd-core/workflows/remove-workspace.md",
+  "gsd-core/workflows/resume-project.md",
+  "gsd-core/workflows/review.md",
+  "gsd-core/workflows/scan.md",
+  "gsd-core/workflows/secure-phase.md",
+  "gsd-core/workflows/session-report.md",
+  "gsd-core/workflows/settings-advanced.md",
+  "gsd-core/workflows/settings-integrations.md",
+  "gsd-core/workflows/settings.md",
+  "gsd-core/workflows/ship.md",
+  "gsd-core/workflows/sketch-wrap-up.md",
+  "gsd-core/workflows/sketch.md",
+  "gsd-core/workflows/smart-entry.md",
+  "gsd-core/workflows/spec-phase.md",
+  "gsd-core/workflows/spike-wrap-up.md",
+  "gsd-core/workflows/spike.md",
+  "gsd-core/workflows/stats.md",
+  "gsd-core/workflows/sync-skills.md",
+  "gsd-core/workflows/thread.md",
+  "gsd-core/workflows/transition.md",
+  "gsd-core/workflows/ui-phase.md",
+  "gsd-core/workflows/ui-review.md",
+  "gsd-core/workflows/ultraplan-phase.md",
+  "gsd-core/workflows/undo.md",
+  "gsd-core/workflows/update.md",
+  "gsd-core/workflows/validate-phase.md",
+  "gsd-core/workflows/verify-phase.md",
+  "gsd-core/workflows/verify-work.md",
+  "hooks/gsd-check-update-worker.js",
+  "hooks/gsd-check-update.js",
+  "hooks/gsd-config-reload.js",
+  "hooks/gsd-context-monitor.js",
+  "hooks/gsd-cursor-post-tool.js",
+  "hooks/gsd-cursor-pre-tool.js",
+  "hooks/gsd-cursor-session-start.js",
+  "hooks/gsd-cursor-stop.js",
+  "hooks/gsd-cursor-subagent-start.js",
+  "hooks/gsd-cursor-subagent-stop.js",
+  "hooks/gsd-ensure-canonical-path.js",
+  "hooks/gsd-graphify-update.sh",
+  "hooks/gsd-phase-boundary.sh",
+  "hooks/gsd-prompt-guard.js",
+  "hooks/gsd-read-guard.js",
+  "hooks/gsd-read-injection-scanner.js",
+  "hooks/gsd-session-state.sh",
+  "hooks/gsd-statusline.js",
+  "hooks/gsd-update-banner.js",
+  "hooks/gsd-validate-commit.sh",
+  "hooks/gsd-windsurf-pre-command.js",
+  "hooks/gsd-windsurf-pre-write.js",
+  "hooks/gsd-workflow-guard.js",
+  "hooks/gsd-worktree-path-guard.js",
+  "hooks/lib/git-cmd.js",
+  "hooks/lib/gsd-graphify-rebuild.sh",
+  "hooks/managed-hooks-registry.cjs",
+  "package.json",
+  "scripts/changeset/README.md",
+  "scripts/changeset/cli.cjs",
+  "scripts/changeset/github-release-notes.cjs",
+  "scripts/changeset/lint.cjs",
+  "scripts/changeset/new.cjs",
+  "scripts/changeset/parse.cjs",
+  "scripts/changeset/render.cjs",
+  "scripts/changeset/serialize.cjs",
+  "scripts/fix-slash-commands.cjs",
+  "scripts/gen-capability-registry.cjs",
+  "scripts/gen-loop-host-contract.cjs",
+  "scripts/lib/allowlist-ratchet.cjs",
+  "scripts/lib/cli-exit.cjs",
+  "skills/gsd-add-tests/SKILL.md",
+  "skills/gsd-ai-integration-phase/SKILL.md",
+  "skills/gsd-audit-fix/SKILL.md",
+  "skills/gsd-audit-milestone/SKILL.md",
+  "skills/gsd-audit-uat/SKILL.md",
+  "skills/gsd-autonomous/SKILL.md",
+  "skills/gsd-capture/SKILL.md",
+  "skills/gsd-cleanup/SKILL.md",
+  "skills/gsd-code-review/SKILL.md",
+  "skills/gsd-complete-milestone/SKILL.md",
+  "skills/gsd-config/SKILL.md",
+  "skills/gsd-debug/SKILL.md",
+  "skills/gsd-discuss-phase/SKILL.md",
+  "skills/gsd-docs-update/SKILL.md",
+  "skills/gsd-eval-review/SKILL.md",
+  "skills/gsd-execute-phase/SKILL.md",
+  "skills/gsd-explore/SKILL.md",
+  "skills/gsd-extract-learnings/SKILL.md",
+  "skills/gsd-fast/SKILL.md",
+  "skills/gsd-forensics/SKILL.md",
+  "skills/gsd-graphify/SKILL.md",
+  "skills/gsd-health/SKILL.md",
+  "skills/gsd-help/SKILL.md",
+  "skills/gsd-import/SKILL.md",
+  "skills/gsd-inbox/SKILL.md",
+  "skills/gsd-ingest-docs/SKILL.md",
+  "skills/gsd-manager/SKILL.md",
+  "skills/gsd-map-codebase/SKILL.md",
+  "skills/gsd-mempalace-capture/SKILL.md",
+  "skills/gsd-mempalace-recall/SKILL.md",
+  "skills/gsd-milestone-summary/SKILL.md",
+  "skills/gsd-mvp-phase/SKILL.md",
+  "skills/gsd-new-milestone/SKILL.md",
+  "skills/gsd-new-project/SKILL.md",
+  "skills/gsd-next/SKILL.md",
+  "skills/gsd-ns-context/SKILL.md",
+  "skills/gsd-ns-ideate/SKILL.md",
+  "skills/gsd-ns-manage/SKILL.md",
+  "skills/gsd-ns-project/SKILL.md",
+  "skills/gsd-ns-review/SKILL.md",
+  "skills/gsd-ns-workflow/SKILL.md",
+  "skills/gsd-onboard/SKILL.md",
+  "skills/gsd-pause-work/SKILL.md",
+  "skills/gsd-phase/SKILL.md",
+  "skills/gsd-plan-phase/SKILL.md",
+  "skills/gsd-plan-review-convergence/SKILL.md",
+  "skills/gsd-pr-branch/SKILL.md",
+  "skills/gsd-profile-user/SKILL.md",
+  "skills/gsd-progress/SKILL.md",
+  "skills/gsd-quick/SKILL.md",
+  "skills/gsd-resume-work/SKILL.md",
+  "skills/gsd-review-backlog/SKILL.md",
+  "skills/gsd-review/SKILL.md",
+  "skills/gsd-secure-phase/SKILL.md",
+  "skills/gsd-settings/SKILL.md",
+  "skills/gsd-ship/SKILL.md",
+  "skills/gsd-sketch/SKILL.md",
+  "skills/gsd-spec-phase/SKILL.md",
+  "skills/gsd-spike/SKILL.md",
+  "skills/gsd-stats/SKILL.md",
+  "skills/gsd-surface/SKILL.md",
+  "skills/gsd-thread/SKILL.md",
+  "skills/gsd-ui-phase/SKILL.md",
+  "skills/gsd-ui-review/SKILL.md",
+  "skills/gsd-ultraplan-phase/SKILL.md",
+  "skills/gsd-undo/SKILL.md",
+  "skills/gsd-update/SKILL.md",
+  "skills/gsd-validate-phase/SKILL.md",
+  "skills/gsd-verify-work/SKILL.md",
+  "skills/gsd-workspace/SKILL.md",
+  "skills/gsd-workstreams/SKILL.md"
+]
diff --git a/tests/fixtures/install-tree/cline.json b/tests/fixtures/install-tree/cline.json
new file mode 100644
index 000000000..668e59098
--- /dev/null
+++ b/tests/fixtures/install-tree/cline.json
@@ -0,0 +1,402 @@
+[
+  ".agents/AGENTS.md",
+  ".clinerules/gsd.md",
+  ".clinerules/hooks/PreToolUse",
+  ".gsd-profile",
+  ".gsd/defaults.json",
+  "agents/gsd-advisor-researcher.md",
+  "agents/gsd-ai-researcher.md",
+  "agents/gsd-assumptions-analyzer.md",
+  "agents/gsd-code-fixer.md",
+  "agents/gsd-code-reviewer.md",
+  "agents/gsd-codebase-mapper.md",
+  "agents/gsd-debug-session-manager.md",
+  "agents/gsd-debugger.md",
+  "agents/gsd-doc-classifier.md",
+  "agents/gsd-doc-synthesizer.md",
+  "agents/gsd-doc-verifier.md",
+  "agents/gsd-doc-writer.md",
+  "agents/gsd-domain-researcher.md",
+  "agents/gsd-eval-auditor.md",
+  "agents/gsd-eval-planner.md",
+  "agents/gsd-executor.md",
+  "agents/gsd-framework-selector.md",
+  "agents/gsd-integration-checker.md",
+  "agents/gsd-intel-updater.md",
+  "agents/gsd-mempalace-curator.md",
+  "agents/gsd-nyquist-auditor.md",
+  "agents/gsd-pattern-mapper.md",
+  "agents/gsd-phase-researcher.md",
+  "agents/gsd-plan-checker.md",
+  "agents/gsd-planner.md",
+  "agents/gsd-project-researcher.md",
+  "agents/gsd-research-synthesizer.md",
+  "agents/gsd-roadmapper.md",
+  "agents/gsd-security-auditor.md",
+  "agents/gsd-ui-auditor.md",
+  "agents/gsd-ui-checker.md",
+  "agents/gsd-ui-researcher.md",
+  "agents/gsd-user-profiler.md",
+  "agents/gsd-verifier.md",
+  "gsd-core/VERSION",
+  "gsd-core/bin/check-latest-version.cjs",
+  "gsd-core/bin/ensure-runtime-build.cjs",
+  "gsd-core/bin/gsd-tools.cjs",
+  "gsd-core/bin/gsd_run",
+  "gsd-core/bin/shared/config-defaults.manifest.json",
+  "gsd-core/bin/shared/config-schema.manifest.json",
+  "gsd-core/bin/shared/model-catalog.json",
+  "gsd-core/bin/shared/runtime-aliases.manifest.json",
+  "gsd-core/bin/verify-reapply-patches.cjs",
+  "gsd-core/contexts/dev.md",
+  "gsd-core/contexts/research.md",
+  "gsd-core/contexts/review.md",
+  "gsd-core/references/agent-contracts.md",
+  "gsd-core/references/agent-skills-bootstrap.md",
+  "gsd-core/references/ai-evals.md",
+  "gsd-core/references/ai-frameworks.md",
+  "gsd-core/references/api-coverage.md",
+  "gsd-core/references/artifact-types.md",
+  "gsd-core/references/autonomous-smart-discuss.md",
+  "gsd-core/references/checkpoints.md",
+  "gsd-core/references/common-bug-patterns.md",
+  "gsd-core/references/context-budget.md",
+  "gsd-core/references/continuation-format.md",
+  "gsd-core/references/debugger-philosophy.md",
+  "gsd-core/references/decimal-phase-calculation.md",
+  "gsd-core/references/doc-conflict-engine.md",
+  "gsd-core/references/domain-probes.md",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/resolutions.json",
+  "gsd-core/references/edge-probe.md",
+  "gsd-core/references/execute-mvp-tdd.md",
+  "gsd-core/references/execute-phase-between-wave-reset.md",
+  "gsd-core/references/execute-phase-context-guard.md",
+  "gsd-core/references/execute-phase-wave-guard.md",
+  "gsd-core/references/executor-examples.md",
+  "gsd-core/references/few-shot-examples/plan-checker.md",
+  "gsd-core/references/few-shot-examples/verifier.md",
+  "gsd-core/references/gate-prompts.md",
+  "gsd-core/references/gates.md",
+  "gsd-core/references/git-integration.md",
+  "gsd-core/references/git-planning-commit.md",
+  "gsd-core/references/gsd-run-resolver.md",
+  "gsd-core/references/honest-verifier.md",
+  "gsd-core/references/ios-scaffold.md",
+  "gsd-core/references/loop-hook-dispatch.md",
+  "gsd-core/references/mandatory-initial-read.md",
+  "gsd-core/references/model-profile-resolution.md",
+  "gsd-core/references/model-profiles.md",
+  "gsd-core/references/mvp-concepts.md",
+  "gsd-core/references/phase-argument-parsing.md",
+  "gsd-core/references/planner-antipatterns.md",
+  "gsd-core/references/planner-chunked.md",
+  "gsd-core/references/planner-gap-closure.md",
+  "gsd-core/references/planner-graphify-auto-update.md",
+  "gsd-core/references/planner-guidance.md",
+  "gsd-core/references/planner-human-verify-mode.md",
+  "gsd-core/references/planner-interface-context.md",
+  "gsd-core/references/planner-load-graph-context.md",
+  "gsd-core/references/planner-mvp-mode.md",
+  "gsd-core/references/planner-reviews.md",
+  "gsd-core/references/planner-revision.md",
+  "gsd-core/references/planner-source-audit.md",
+  "gsd-core/references/planning-config.md",
+  "gsd-core/references/prohibition-probe-fixtures/01-streak-reminder/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/02-clean-utility/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/03-multi-prohibition/expected.json",
+  "gsd-core/references/prohibition-probe.md",
+  "gsd-core/references/project-skills-discovery.md",
+  "gsd-core/references/questioning.md",
+  "gsd-core/references/research-documentation-lookup.md",
+  "gsd-core/references/research-philosophy.md",
+  "gsd-core/references/research-verification-protocol.md",
+  "gsd-core/references/reviewer-instances.md",
+  "gsd-core/references/revision-loop.md",
+  "gsd-core/references/scout-codebase.md",
+  "gsd-core/references/security-asvs-levels.md",
+  "gsd-core/references/skeleton-template.md",
+  "gsd-core/references/sketch-interactivity.md",
+  "gsd-core/references/sketch-theme-system.md",
+  "gsd-core/references/sketch-tooling.md",
+  "gsd-core/references/sketch-variant-patterns.md",
+  "gsd-core/references/specless-probe-fallback.md",
+  "gsd-core/references/spidr-splitting.md",
+  "gsd-core/references/tdd.md",
+  "gsd-core/references/thinking-models-debug.md",
+  "gsd-core/references/thinking-models-execution.md",
+  "gsd-core/references/thinking-models-planning.md",
+  "gsd-core/references/thinking-models-research.md",
+  "gsd-core/references/thinking-models-verification.md",
+  "gsd-core/references/thinking-partner.md",
+  "gsd-core/references/ui-brand.md",
+  "gsd-core/references/ui-consideration-probe.md",
+  "gsd-core/references/universal-anti-patterns.md",
+  "gsd-core/references/untrusted-input-boundary.md",
+  "gsd-core/references/user-profiling.md",
+  "gsd-core/references/user-story-template.md",
+  "gsd-core/references/verification-overrides.md",
+  "gsd-core/references/verification-patterns.md",
+  "gsd-core/references/verify-mvp-mode.md",
+  "gsd-core/references/workstream-flag.md",
+  "gsd-core/references/worktree-branch-check.md",
+  "gsd-core/references/worktree-path-safety.md",
+  "gsd-core/templates/AI-SPEC.md",
+  "gsd-core/templates/DEBUG.md",
+  "gsd-core/templates/README.md",
+  "gsd-core/templates/SECURITY.md",
+  "gsd-core/templates/UAT.md",
+  "gsd-core/templates/UI-SPEC.md",
+  "gsd-core/templates/VALIDATION.md",
+  "gsd-core/templates/claude-md.md",
+  "gsd-core/templates/codebase/architecture.md",
+  "gsd-core/templates/codebase/concerns.md",
+  "gsd-core/templates/codebase/conventions.md",
+  "gsd-core/templates/codebase/integrations.md",
+  "gsd-core/templates/codebase/stack.md",
+  "gsd-core/templates/codebase/structure.md",
+  "gsd-core/templates/codebase/testing.md",
+  "gsd-core/templates/config.json",
+  "gsd-core/templates/context.md",
+  "gsd-core/templates/continue-here.md",
+  "gsd-core/templates/copilot-instructions.md",
+  "gsd-core/templates/debug-subagent-prompt.md",
+  "gsd-core/templates/dev-preferences.md",
+  "gsd-core/templates/discovery.md",
+  "gsd-core/templates/discussion-log.md",
+  "gsd-core/templates/milestone-archive.md",
+  "gsd-core/templates/milestone.md",
+  "gsd-core/templates/phase-prompt.md",
+  "gsd-core/templates/planner-subagent-prompt.md",
+  "gsd-core/templates/project.md",
+  "gsd-core/templates/requirements.md",
+  "gsd-core/templates/research-project/ARCHITECTURE.md",
+  "gsd-core/templates/research-project/FEATURES.md",
+  "gsd-core/templates/research-project/PITFALLS.md",
+  "gsd-core/templates/research-project/STACK.md",
+  "gsd-core/templates/research-project/SUMMARY.md",
+  "gsd-core/templates/research.md",
+  "gsd-core/templates/retrospective.md",
+  "gsd-core/templates/roadmap.md",
+  "gsd-core/templates/spec.md",
+  "gsd-core/templates/state.md",
+  "gsd-core/templates/summary-complex.md",
+  "gsd-core/templates/summary-minimal.md",
+  "gsd-core/templates/summary-standard.md",
+  "gsd-core/templates/summary.md",
+  "gsd-core/templates/user-profile.md",
+  "gsd-core/templates/user-setup.md",
+  "gsd-core/templates/verification-report.md",
+  "gsd-core/workflows/_runtime-launcher.snippet.sh",
+  "gsd-core/workflows/add-backlog.md",
+  "gsd-core/workflows/add-phase.md",
+  "gsd-core/workflows/add-tests.md",
+  "gsd-core/workflows/add-todo.md",
+  "gsd-core/workflows/ai-integration-phase.md",
+  "gsd-core/workflows/analyze-dependencies.md",
+  "gsd-core/workflows/audit-fix.md",
+  "gsd-core/workflows/audit-milestone.md",
+  "gsd-core/workflows/audit-uat.md",
+  "gsd-core/workflows/autonomous.md",
+  "gsd-core/workflows/check-todos.md",
+  "gsd-core/workflows/cleanup.md",
+  "gsd-core/workflows/code-review-fix.md",
+  "gsd-core/workflows/code-review.md",
+  "gsd-core/workflows/complete-milestone.md",
+  "gsd-core/workflows/debug.md",
+  "gsd-core/workflows/diagnose-issues.md",
+  "gsd-core/workflows/discovery-phase.md",
+  "gsd-core/workflows/discuss-phase-assumptions.md",
+  "gsd-core/workflows/discuss-phase-power.md",
+  "gsd-core/workflows/discuss-phase.md",
+  "gsd-core/workflows/discuss-phase/modes/advisor.md",
+  "gsd-core/workflows/discuss-phase/modes/all.md",
+  "gsd-core/workflows/discuss-phase/modes/analyze.md",
+  "gsd-core/workflows/discuss-phase/modes/auto.md",
+  "gsd-core/workflows/discuss-phase/modes/batch.md",
+  "gsd-core/workflows/discuss-phase/modes/chain.md",
+  "gsd-core/workflows/discuss-phase/modes/default.md",
+  "gsd-core/workflows/discuss-phase/modes/power.md",
+  "gsd-core/workflows/discuss-phase/modes/text.md",
+  "gsd-core/workflows/discuss-phase/templates/checkpoint.json",
+  "gsd-core/workflows/discuss-phase/templates/context.md",
+  "gsd-core/workflows/discuss-phase/templates/discussion-log.md",
+  "gsd-core/workflows/do.md",
+  "gsd-core/workflows/docs-update.md",
+  "gsd-core/workflows/edit-phase.md",
+  "gsd-core/workflows/eval-review.md",
+  "gsd-core/workflows/execute-phase.md",
+  "gsd-core/workflows/execute-phase/steps/codebase-drift-gate.md",
+  "gsd-core/workflows/execute-phase/steps/per-plan-worktree-gate.md",
+  "gsd-core/workflows/execute-phase/steps/post-merge-gate.md",
+  "gsd-core/workflows/execute-phase/steps/regression-gate.md",
+  "gsd-core/workflows/execute-phase/steps/worktree-recovery-policy.md",
+  "gsd-core/workflows/execute-plan.md",
+  "gsd-core/workflows/explore.md",
+  "gsd-core/workflows/extract-learnings.md",
+  "gsd-core/workflows/fast.md",
+  "gsd-core/workflows/forensics.md",
+  "gsd-core/workflows/graduation.md",
+  "gsd-core/workflows/health.md",
+  "gsd-core/workflows/help.md",
+  "gsd-core/workflows/help/modes/brief.md",
+  "gsd-core/workflows/help/modes/default.md",
+  "gsd-core/workflows/help/modes/full.md",
+  "gsd-core/workflows/help/modes/topic.md",
+  "gsd-core/workflows/import.md",
+  "gsd-core/workflows/inbox.md",
+  "gsd-core/workflows/ingest-docs.md",
+  "gsd-core/workflows/insert-phase.md",
+  "gsd-core/workflows/list-phase-assumptions.md",
+  "gsd-core/workflows/list-seeds.md",
+  "gsd-core/workflows/list-workspaces.md",
+  "gsd-core/workflows/manager.md",
+  "gsd-core/workflows/map-codebase.md",
+  "gsd-core/workflows/milestone-summary.md",
+  "gsd-core/workflows/mvp-phase.md",
+  "gsd-core/workflows/new-milestone.md",
+  "gsd-core/workflows/new-project.md",
+  "gsd-core/workflows/new-workspace.md",
+  "gsd-core/workflows/next.md",
+  "gsd-core/workflows/node-repair.md",
+  "gsd-core/workflows/note.md",
+  "gsd-core/workflows/onboard.md",
+  "gsd-core/workflows/pause-work.md",
+  "gsd-core/workflows/plan-milestone-gaps.md",
+  "gsd-core/workflows/plan-phase.md",
+  "gsd-core/workflows/plan-phase/steps/closed-phase-gate.md",
+  "gsd-core/workflows/plan-phase/steps/prd-express-path.md",
+  "gsd-core/workflows/plan-phase/steps/windows-troubleshooting.md",
+  "gsd-core/workflows/plan-review-convergence.md",
+  "gsd-core/workflows/plant-seed.md",
+  "gsd-core/workflows/pr-branch.md",
+  "gsd-core/workflows/profile-user.md",
+  "gsd-core/workflows/progress.md",
+  "gsd-core/workflows/quick.md",
+  "gsd-core/workflows/reapply-patches.md",
+  "gsd-core/workflows/remove-phase.md",
+  "gsd-core/workflows/remove-workspace.md",
+  "gsd-core/workflows/resume-project.md",
+  "gsd-core/workflows/review.md",
+  "gsd-core/workflows/scan.md",
+  "gsd-core/workflows/secure-phase.md",
+  "gsd-core/workflows/session-report.md",
+  "gsd-core/workflows/settings-advanced.md",
+  "gsd-core/workflows/settings-integrations.md",
+  "gsd-core/workflows/settings.md",
+  "gsd-core/workflows/ship.md",
+  "gsd-core/workflows/sketch-wrap-up.md",
+  "gsd-core/workflows/sketch.md",
+  "gsd-core/workflows/smart-entry.md",
+  "gsd-core/workflows/spec-phase.md",
+  "gsd-core/workflows/spike-wrap-up.md",
+  "gsd-core/workflows/spike.md",
+  "gsd-core/workflows/stats.md",
+  "gsd-core/workflows/sync-skills.md",
+  "gsd-core/workflows/thread.md",
+  "gsd-core/workflows/transition.md",
+  "gsd-core/workflows/ui-phase.md",
+  "gsd-core/workflows/ui-review.md",
+  "gsd-core/workflows/ultraplan-phase.md",
+  "gsd-core/workflows/undo.md",
+  "gsd-core/workflows/update.md",
+  "gsd-core/workflows/validate-phase.md",
+  "gsd-core/workflows/verify-phase.md",
+  "gsd-core/workflows/verify-work.md",
+  "scripts/changeset/README.md",
+  "scripts/changeset/cli.cjs",
+  "scripts/changeset/github-release-notes.cjs",
+  "scripts/changeset/lint.cjs",
+  "scripts/changeset/new.cjs",
+  "scripts/changeset/parse.cjs",
+  "scripts/changeset/render.cjs",
+  "scripts/changeset/serialize.cjs",
+  "scripts/fix-slash-commands.cjs",
+  "scripts/gen-capability-registry.cjs",
+  "scripts/gen-loop-host-contract.cjs",
+  "scripts/lib/allowlist-ratchet.cjs",
+  "scripts/lib/cli-exit.cjs",
+  "skills/gsd-ns-context/SKILL.md",
+  "skills/gsd-ns-context/skills/docs-update/SKILL.md",
+  "skills/gsd-ns-context/skills/extract-learnings/SKILL.md",
+  "skills/gsd-ns-context/skills/graphify/SKILL.md",
+  "skills/gsd-ns-context/skills/map-codebase/SKILL.md",
+  "skills/gsd-ns-context/skills/mempalace-capture/SKILL.md",
+  "skills/gsd-ns-context/skills/mempalace-recall/SKILL.md",
+  "skills/gsd-ns-ideate/SKILL.md",
+  "skills/gsd-ns-ideate/skills/capture/SKILL.md",
+  "skills/gsd-ns-ideate/skills/explore/SKILL.md",
+  "skills/gsd-ns-ideate/skills/sketch/SKILL.md",
+  "skills/gsd-ns-ideate/skills/spec-phase/SKILL.md",
+  "skills/gsd-ns-ideate/skills/spike/SKILL.md",
+  "skills/gsd-ns-manage/SKILL.md",
+  "skills/gsd-ns-manage/skills/cleanup/SKILL.md",
+  "skills/gsd-ns-manage/skills/config/SKILL.md",
+  "skills/gsd-ns-manage/skills/health/SKILL.md",
+  "skills/gsd-ns-manage/skills/help/SKILL.md",
+  "skills/gsd-ns-manage/skills/inbox/SKILL.md",
+  "skills/gsd-ns-manage/skills/manager/SKILL.md",
+  "skills/gsd-ns-manage/skills/pause-work/SKILL.md",
+  "skills/gsd-ns-manage/skills/pr-branch/SKILL.md",
+  "skills/gsd-ns-manage/skills/resume-work/SKILL.md",
+  "skills/gsd-ns-manage/skills/settings/SKILL.md",
+  "skills/gsd-ns-manage/skills/ship/SKILL.md",
+  "skills/gsd-ns-manage/skills/stats/SKILL.md",
+  "skills/gsd-ns-manage/skills/surface/SKILL.md",
+  "skills/gsd-ns-manage/skills/thread/SKILL.md",
+  "skills/gsd-ns-manage/skills/undo/SKILL.md",
+  "skills/gsd-ns-manage/skills/update/SKILL.md",
+  "skills/gsd-ns-manage/skills/workspace/SKILL.md",
+  "skills/gsd-ns-manage/skills/workstreams/SKILL.md",
+  "skills/gsd-ns-project/SKILL.md",
+  "skills/gsd-ns-project/skills/audit-milestone/SKILL.md",
+  "skills/gsd-ns-project/skills/complete-milestone/SKILL.md",
+  "skills/gsd-ns-project/skills/import/SKILL.md",
+  "skills/gsd-ns-project/skills/ingest-docs/SKILL.md",
+  "skills/gsd-ns-project/skills/milestone-summary/SKILL.md",
+  "skills/gsd-ns-project/skills/new-milestone/SKILL.md",
+  "skills/gsd-ns-project/skills/new-project/SKILL.md",
+  "skills/gsd-ns-project/skills/onboard/SKILL.md",
+  "skills/gsd-ns-project/skills/profile-user/SKILL.md",
+  "skills/gsd-ns-project/skills/review-backlog/SKILL.md",
+  "skills/gsd-ns-review/SKILL.md",
+  "skills/gsd-ns-review/skills/audit-fix/SKILL.md",
+  "skills/gsd-ns-review/skills/audit-uat/SKILL.md",
+  "skills/gsd-ns-review/skills/code-review/SKILL.md",
+  "skills/gsd-ns-review/skills/debug/SKILL.md",
+  "skills/gsd-ns-review/skills/eval-review/SKILL.md",
+  "skills/gsd-ns-review/skills/forensics/SKILL.md",
+  "skills/gsd-ns-review/skills/review/SKILL.md",
+  "skills/gsd-ns-review/skills/secure-phase/SKILL.md",
+  "skills/gsd-ns-review/skills/ui-phase/SKILL.md",
+  "skills/gsd-ns-review/skills/ui-review/SKILL.md",
+  "skills/gsd-ns-review/skills/validate-phase/SKILL.md",
+  "skills/gsd-ns-workflow/SKILL.md",
+  "skills/gsd-ns-workflow/skills/add-tests/SKILL.md",
+  "skills/gsd-ns-workflow/skills/ai-integration-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/autonomous/SKILL.md",
+  "skills/gsd-ns-workflow/skills/discuss-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/execute-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/fast/SKILL.md",
+  "skills/gsd-ns-workflow/skills/mvp-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/next/SKILL.md",
+  "skills/gsd-ns-workflow/skills/phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/plan-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/plan-review-convergence/SKILL.md",
+  "skills/gsd-ns-workflow/skills/progress/SKILL.md",
+  "skills/gsd-ns-workflow/skills/quick/SKILL.md",
+  "skills/gsd-ns-workflow/skills/spec-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/ultraplan-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/verify-work/SKILL.md"
+]
diff --git a/tests/fixtures/install-tree/codebuddy.json b/tests/fixtures/install-tree/codebuddy.json
new file mode 100644
index 000000000..dcc5e54bc
--- /dev/null
+++ b/tests/fixtures/install-tree/codebuddy.json
@@ -0,0 +1,497 @@
+[
+  ".gsd-profile",
+  ".gsd/defaults.json",
+  "agents/gsd-advisor-researcher.md",
+  "agents/gsd-ai-researcher.md",
+  "agents/gsd-assumptions-analyzer.md",
+  "agents/gsd-code-fixer.md",
+  "agents/gsd-code-reviewer.md",
+  "agents/gsd-codebase-mapper.md",
+  "agents/gsd-debug-session-manager.md",
+  "agents/gsd-debugger.md",
+  "agents/gsd-doc-classifier.md",
+  "agents/gsd-doc-synthesizer.md",
+  "agents/gsd-doc-verifier.md",
+  "agents/gsd-doc-writer.md",
+  "agents/gsd-domain-researcher.md",
+  "agents/gsd-eval-auditor.md",
+  "agents/gsd-eval-planner.md",
+  "agents/gsd-executor.md",
+  "agents/gsd-framework-selector.md",
+  "agents/gsd-integration-checker.md",
+  "agents/gsd-intel-updater.md",
+  "agents/gsd-mempalace-curator.md",
+  "agents/gsd-nyquist-auditor.md",
+  "agents/gsd-pattern-mapper.md",
+  "agents/gsd-phase-researcher.md",
+  "agents/gsd-plan-checker.md",
+  "agents/gsd-planner.md",
+  "agents/gsd-project-researcher.md",
+  "agents/gsd-research-synthesizer.md",
+  "agents/gsd-roadmapper.md",
+  "agents/gsd-security-auditor.md",
+  "agents/gsd-ui-auditor.md",
+  "agents/gsd-ui-checker.md",
+  "agents/gsd-ui-researcher.md",
+  "agents/gsd-user-profiler.md",
+  "agents/gsd-verifier.md",
+  "commands/gsd-add-tests.md",
+  "commands/gsd-ai-integration-phase.md",
+  "commands/gsd-audit-fix.md",
+  "commands/gsd-audit-milestone.md",
+  "commands/gsd-audit-uat.md",
+  "commands/gsd-autonomous.md",
+  "commands/gsd-capture.md",
+  "commands/gsd-cleanup.md",
+  "commands/gsd-code-review.md",
+  "commands/gsd-complete-milestone.md",
+  "commands/gsd-config.md",
+  "commands/gsd-debug.md",
+  "commands/gsd-discuss-phase.md",
+  "commands/gsd-docs-update.md",
+  "commands/gsd-eval-review.md",
+  "commands/gsd-execute-phase.md",
+  "commands/gsd-explore.md",
+  "commands/gsd-extract-learnings.md",
+  "commands/gsd-fast.md",
+  "commands/gsd-forensics.md",
+  "commands/gsd-graphify.md",
+  "commands/gsd-health.md",
+  "commands/gsd-help.md",
+  "commands/gsd-import.md",
+  "commands/gsd-inbox.md",
+  "commands/gsd-ingest-docs.md",
+  "commands/gsd-manager.md",
+  "commands/gsd-map-codebase.md",
+  "commands/gsd-mempalace-capture.md",
+  "commands/gsd-mempalace-recall.md",
+  "commands/gsd-milestone-summary.md",
+  "commands/gsd-mvp-phase.md",
+  "commands/gsd-new-milestone.md",
+  "commands/gsd-new-project.md",
+  "commands/gsd-next.md",
+  "commands/gsd-ns-context.md",
+  "commands/gsd-ns-ideate.md",
+  "commands/gsd-ns-manage.md",
+  "commands/gsd-ns-project.md",
+  "commands/gsd-ns-review.md",
+  "commands/gsd-ns-workflow.md",
+  "commands/gsd-onboard.md",
+  "commands/gsd-pause-work.md",
+  "commands/gsd-phase.md",
+  "commands/gsd-plan-phase.md",
+  "commands/gsd-plan-review-convergence.md",
+  "commands/gsd-pr-branch.md",
+  "commands/gsd-profile-user.md",
+  "commands/gsd-progress.md",
+  "commands/gsd-quick.md",
+  "commands/gsd-resume-work.md",
+  "commands/gsd-review-backlog.md",
+  "commands/gsd-review.md",
+  "commands/gsd-secure-phase.md",
+  "commands/gsd-settings.md",
+  "commands/gsd-ship.md",
+  "commands/gsd-sketch.md",
+  "commands/gsd-spec-phase.md",
+  "commands/gsd-spike.md",
+  "commands/gsd-stats.md",
+  "commands/gsd-surface.md",
+  "commands/gsd-thread.md",
+  "commands/gsd-ui-phase.md",
+  "commands/gsd-ui-review.md",
+  "commands/gsd-ultraplan-phase.md",
+  "commands/gsd-undo.md",
+  "commands/gsd-update.md",
+  "commands/gsd-validate-phase.md",
+  "commands/gsd-verify-work.md",
+  "commands/gsd-workspace.md",
+  "commands/gsd-workstreams.md",
+  "gsd-core/VERSION",
+  "gsd-core/bin/check-latest-version.cjs",
+  "gsd-core/bin/ensure-runtime-build.cjs",
+  "gsd-core/bin/gsd-tools.cjs",
+  "gsd-core/bin/gsd_run",
+  "gsd-core/bin/shared/config-defaults.manifest.json",
+  "gsd-core/bin/shared/config-schema.manifest.json",
+  "gsd-core/bin/shared/model-catalog.json",
+  "gsd-core/bin/shared/runtime-aliases.manifest.json",
+  "gsd-core/bin/verify-reapply-patches.cjs",
+  "gsd-core/contexts/dev.md",
+  "gsd-core/contexts/research.md",
+  "gsd-core/contexts/review.md",
+  "gsd-core/references/agent-contracts.md",
+  "gsd-core/references/agent-skills-bootstrap.md",
+  "gsd-core/references/ai-evals.md",
+  "gsd-core/references/ai-frameworks.md",
+  "gsd-core/references/api-coverage.md",
+  "gsd-core/references/artifact-types.md",
+  "gsd-core/references/autonomous-smart-discuss.md",
+  "gsd-core/references/checkpoints.md",
+  "gsd-core/references/common-bug-patterns.md",
+  "gsd-core/references/context-budget.md",
+  "gsd-core/references/continuation-format.md",
+  "gsd-core/references/debugger-philosophy.md",
+  "gsd-core/references/decimal-phase-calculation.md",
+  "gsd-core/references/doc-conflict-engine.md",
+  "gsd-core/references/domain-probes.md",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/resolutions.json",
+  "gsd-core/references/edge-probe.md",
+  "gsd-core/references/execute-mvp-tdd.md",
+  "gsd-core/references/execute-phase-between-wave-reset.md",
+  "gsd-core/references/execute-phase-context-guard.md",
+  "gsd-core/references/execute-phase-wave-guard.md",
+  "gsd-core/references/executor-examples.md",
+  "gsd-core/references/few-shot-examples/plan-checker.md",
+  "gsd-core/references/few-shot-examples/verifier.md",
+  "gsd-core/references/gate-prompts.md",
+  "gsd-core/references/gates.md",
+  "gsd-core/references/git-integration.md",
+  "gsd-core/references/git-planning-commit.md",
+  "gsd-core/references/gsd-run-resolver.md",
+  "gsd-core/references/honest-verifier.md",
+  "gsd-core/references/ios-scaffold.md",
+  "gsd-core/references/loop-hook-dispatch.md",
+  "gsd-core/references/mandatory-initial-read.md",
+  "gsd-core/references/model-profile-resolution.md",
+  "gsd-core/references/model-profiles.md",
+  "gsd-core/references/mvp-concepts.md",
+  "gsd-core/references/phase-argument-parsing.md",
+  "gsd-core/references/planner-antipatterns.md",
+  "gsd-core/references/planner-chunked.md",
+  "gsd-core/references/planner-gap-closure.md",
+  "gsd-core/references/planner-graphify-auto-update.md",
+  "gsd-core/references/planner-guidance.md",
+  "gsd-core/references/planner-human-verify-mode.md",
+  "gsd-core/references/planner-interface-context.md",
+  "gsd-core/references/planner-load-graph-context.md",
+  "gsd-core/references/planner-mvp-mode.md",
+  "gsd-core/references/planner-reviews.md",
+  "gsd-core/references/planner-revision.md",
+  "gsd-core/references/planner-source-audit.md",
+  "gsd-core/references/planning-config.md",
+  "gsd-core/references/prohibition-probe-fixtures/01-streak-reminder/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/02-clean-utility/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/03-multi-prohibition/expected.json",
+  "gsd-core/references/prohibition-probe.md",
+  "gsd-core/references/project-skills-discovery.md",
+  "gsd-core/references/questioning.md",
+  "gsd-core/references/research-documentation-lookup.md",
+  "gsd-core/references/research-philosophy.md",
+  "gsd-core/references/research-verification-protocol.md",
+  "gsd-core/references/reviewer-instances.md",
+  "gsd-core/references/revision-loop.md",
+  "gsd-core/references/scout-codebase.md",
+  "gsd-core/references/security-asvs-levels.md",
+  "gsd-core/references/skeleton-template.md",
+  "gsd-core/references/sketch-interactivity.md",
+  "gsd-core/references/sketch-theme-system.md",
+  "gsd-core/references/sketch-tooling.md",
+  "gsd-core/references/sketch-variant-patterns.md",
+  "gsd-core/references/specless-probe-fallback.md",
+  "gsd-core/references/spidr-splitting.md",
+  "gsd-core/references/tdd.md",
+  "gsd-core/references/thinking-models-debug.md",
+  "gsd-core/references/thinking-models-execution.md",
+  "gsd-core/references/thinking-models-planning.md",
+  "gsd-core/references/thinking-models-research.md",
+  "gsd-core/references/thinking-models-verification.md",
+  "gsd-core/references/thinking-partner.md",
+  "gsd-core/references/ui-brand.md",
+  "gsd-core/references/ui-consideration-probe.md",
+  "gsd-core/references/universal-anti-patterns.md",
+  "gsd-core/references/untrusted-input-boundary.md",
+  "gsd-core/references/user-profiling.md",
+  "gsd-core/references/user-story-template.md",
+  "gsd-core/references/verification-overrides.md",
+  "gsd-core/references/verification-patterns.md",
+  "gsd-core/references/verify-mvp-mode.md",
+  "gsd-core/references/workstream-flag.md",
+  "gsd-core/references/worktree-branch-check.md",
+  "gsd-core/references/worktree-path-safety.md",
+  "gsd-core/templates/AI-SPEC.md",
+  "gsd-core/templates/DEBUG.md",
+  "gsd-core/templates/README.md",
+  "gsd-core/templates/SECURITY.md",
+  "gsd-core/templates/UAT.md",
+  "gsd-core/templates/UI-SPEC.md",
+  "gsd-core/templates/VALIDATION.md",
+  "gsd-core/templates/claude-md.md",
+  "gsd-core/templates/codebase/architecture.md",
+  "gsd-core/templates/codebase/concerns.md",
+  "gsd-core/templates/codebase/conventions.md",
+  "gsd-core/templates/codebase/integrations.md",
+  "gsd-core/templates/codebase/stack.md",
+  "gsd-core/templates/codebase/structure.md",
+  "gsd-core/templates/codebase/testing.md",
+  "gsd-core/templates/config.json",
+  "gsd-core/templates/context.md",
+  "gsd-core/templates/continue-here.md",
+  "gsd-core/templates/copilot-instructions.md",
+  "gsd-core/templates/debug-subagent-prompt.md",
+  "gsd-core/templates/dev-preferences.md",
+  "gsd-core/templates/discovery.md",
+  "gsd-core/templates/discussion-log.md",
+  "gsd-core/templates/milestone-archive.md",
+  "gsd-core/templates/milestone.md",
+  "gsd-core/templates/phase-prompt.md",
+  "gsd-core/templates/planner-subagent-prompt.md",
+  "gsd-core/templates/project.md",
+  "gsd-core/templates/requirements.md",
+  "gsd-core/templates/research-project/ARCHITECTURE.md",
+  "gsd-core/templates/research-project/FEATURES.md",
+  "gsd-core/templates/research-project/PITFALLS.md",
+  "gsd-core/templates/research-project/STACK.md",
+  "gsd-core/templates/research-project/SUMMARY.md",
+  "gsd-core/templates/research.md",
+  "gsd-core/templates/retrospective.md",
+  "gsd-core/templates/roadmap.md",
+  "gsd-core/templates/spec.md",
+  "gsd-core/templates/state.md",
+  "gsd-core/templates/summary-complex.md",
+  "gsd-core/templates/summary-minimal.md",
+  "gsd-core/templates/summary-standard.md",
+  "gsd-core/templates/summary.md",
+  "gsd-core/templates/user-profile.md",
+  "gsd-core/templates/user-setup.md",
+  "gsd-core/templates/verification-report.md",
+  "gsd-core/workflows/_runtime-launcher.snippet.sh",
+  "gsd-core/workflows/add-backlog.md",
+  "gsd-core/workflows/add-phase.md",
+  "gsd-core/workflows/add-tests.md",
+  "gsd-core/workflows/add-todo.md",
+  "gsd-core/workflows/ai-integration-phase.md",
+  "gsd-core/workflows/analyze-dependencies.md",
+  "gsd-core/workflows/audit-fix.md",
+  "gsd-core/workflows/audit-milestone.md",
+  "gsd-core/workflows/audit-uat.md",
+  "gsd-core/workflows/autonomous.md",
+  "gsd-core/workflows/check-todos.md",
+  "gsd-core/workflows/cleanup.md",
+  "gsd-core/workflows/code-review-fix.md",
+  "gsd-core/workflows/code-review.md",
+  "gsd-core/workflows/complete-milestone.md",
+  "gsd-core/workflows/debug.md",
+  "gsd-core/workflows/diagnose-issues.md",
+  "gsd-core/workflows/discovery-phase.md",
+  "gsd-core/workflows/discuss-phase-assumptions.md",
+  "gsd-core/workflows/discuss-phase-power.md",
+  "gsd-core/workflows/discuss-phase.md",
+  "gsd-core/workflows/discuss-phase/modes/advisor.md",
+  "gsd-core/workflows/discuss-phase/modes/all.md",
+  "gsd-core/workflows/discuss-phase/modes/analyze.md",
+  "gsd-core/workflows/discuss-phase/modes/auto.md",
+  "gsd-core/workflows/discuss-phase/modes/batch.md",
+  "gsd-core/workflows/discuss-phase/modes/chain.md",
+  "gsd-core/workflows/discuss-phase/modes/default.md",
+  "gsd-core/workflows/discuss-phase/modes/power.md",
+  "gsd-core/workflows/discuss-phase/modes/text.md",
+  "gsd-core/workflows/discuss-phase/templates/checkpoint.json",
+  "gsd-core/workflows/discuss-phase/templates/context.md",
+  "gsd-core/workflows/discuss-phase/templates/discussion-log.md",
+  "gsd-core/workflows/do.md",
+  "gsd-core/workflows/docs-update.md",
+  "gsd-core/workflows/edit-phase.md",
+  "gsd-core/workflows/eval-review.md",
+  "gsd-core/workflows/execute-phase.md",
+  "gsd-core/workflows/execute-phase/steps/codebase-drift-gate.md",
+  "gsd-core/workflows/execute-phase/steps/per-plan-worktree-gate.md",
+  "gsd-core/workflows/execute-phase/steps/post-merge-gate.md",
+  "gsd-core/workflows/execute-phase/steps/regression-gate.md",
+  "gsd-core/workflows/execute-phase/steps/worktree-recovery-policy.md",
+  "gsd-core/workflows/execute-plan.md",
+  "gsd-core/workflows/explore.md",
+  "gsd-core/workflows/extract-learnings.md",
+  "gsd-core/workflows/fast.md",
+  "gsd-core/workflows/forensics.md",
+  "gsd-core/workflows/graduation.md",
+  "gsd-core/workflows/health.md",
+  "gsd-core/workflows/help.md",
+  "gsd-core/workflows/help/modes/brief.md",
+  "gsd-core/workflows/help/modes/default.md",
+  "gsd-core/workflows/help/modes/full.md",
+  "gsd-core/workflows/help/modes/topic.md",
+  "gsd-core/workflows/import.md",
+  "gsd-core/workflows/inbox.md",
+  "gsd-core/workflows/ingest-docs.md",
+  "gsd-core/workflows/insert-phase.md",
+  "gsd-core/workflows/list-phase-assumptions.md",
+  "gsd-core/workflows/list-seeds.md",
+  "gsd-core/workflows/list-workspaces.md",
+  "gsd-core/workflows/manager.md",
+  "gsd-core/workflows/map-codebase.md",
+  "gsd-core/workflows/milestone-summary.md",
+  "gsd-core/workflows/mvp-phase.md",
+  "gsd-core/workflows/new-milestone.md",
+  "gsd-core/workflows/new-project.md",
+  "gsd-core/workflows/new-workspace.md",
+  "gsd-core/workflows/next.md",
+  "gsd-core/workflows/node-repair.md",
+  "gsd-core/workflows/note.md",
+  "gsd-core/workflows/onboard.md",
+  "gsd-core/workflows/pause-work.md",
+  "gsd-core/workflows/plan-milestone-gaps.md",
+  "gsd-core/workflows/plan-phase.md",
+  "gsd-core/workflows/plan-phase/steps/closed-phase-gate.md",
+  "gsd-core/workflows/plan-phase/steps/prd-express-path.md",
+  "gsd-core/workflows/plan-phase/steps/windows-troubleshooting.md",
+  "gsd-core/workflows/plan-review-convergence.md",
+  "gsd-core/workflows/plant-seed.md",
+  "gsd-core/workflows/pr-branch.md",
+  "gsd-core/workflows/profile-user.md",
+  "gsd-core/workflows/progress.md",
+  "gsd-core/workflows/quick.md",
+  "gsd-core/workflows/reapply-patches.md",
+  "gsd-core/workflows/remove-phase.md",
+  "gsd-core/workflows/remove-workspace.md",
+  "gsd-core/workflows/resume-project.md",
+  "gsd-core/workflows/review.md",
+  "gsd-core/workflows/scan.md",
+  "gsd-core/workflows/secure-phase.md",
+  "gsd-core/workflows/session-report.md",
+  "gsd-core/workflows/settings-advanced.md",
+  "gsd-core/workflows/settings-integrations.md",
+  "gsd-core/workflows/settings.md",
+  "gsd-core/workflows/ship.md",
+  "gsd-core/workflows/sketch-wrap-up.md",
+  "gsd-core/workflows/sketch.md",
+  "gsd-core/workflows/smart-entry.md",
+  "gsd-core/workflows/spec-phase.md",
+  "gsd-core/workflows/spike-wrap-up.md",
+  "gsd-core/workflows/spike.md",
+  "gsd-core/workflows/stats.md",
+  "gsd-core/workflows/sync-skills.md",
+  "gsd-core/workflows/thread.md",
+  "gsd-core/workflows/transition.md",
+  "gsd-core/workflows/ui-phase.md",
+  "gsd-core/workflows/ui-review.md",
+  "gsd-core/workflows/ultraplan-phase.md",
+  "gsd-core/workflows/undo.md",
+  "gsd-core/workflows/update.md",
+  "gsd-core/workflows/validate-phase.md",
+  "gsd-core/workflows/verify-phase.md",
+  "gsd-core/workflows/verify-work.md",
+  "hooks/gsd-check-update-worker.js",
+  "hooks/gsd-check-update.js",
+  "hooks/gsd-config-reload.js",
+  "hooks/gsd-context-monitor.js",
+  "hooks/gsd-cursor-post-tool.js",
+  "hooks/gsd-cursor-pre-tool.js",
+  "hooks/gsd-cursor-session-start.js",
+  "hooks/gsd-cursor-stop.js",
+  "hooks/gsd-cursor-subagent-start.js",
+  "hooks/gsd-cursor-subagent-stop.js",
+  "hooks/gsd-ensure-canonical-path.js",
+  "hooks/gsd-graphify-update.sh",
+  "hooks/gsd-phase-boundary.sh",
+  "hooks/gsd-prompt-guard.js",
+  "hooks/gsd-read-guard.js",
+  "hooks/gsd-read-injection-scanner.js",
+  "hooks/gsd-session-state.sh",
+  "hooks/gsd-statusline.js",
+  "hooks/gsd-update-banner.js",
+  "hooks/gsd-validate-commit.sh",
+  "hooks/gsd-windsurf-pre-command.js",
+  "hooks/gsd-windsurf-pre-write.js",
+  "hooks/gsd-workflow-guard.js",
+  "hooks/gsd-worktree-path-guard.js",
+  "hooks/lib/git-cmd.js",
+  "hooks/lib/gsd-graphify-rebuild.sh",
+  "hooks/managed-hooks-registry.cjs",
+  "package.json",
+  "scripts/changeset/README.md",
+  "scripts/changeset/cli.cjs",
+  "scripts/changeset/github-release-notes.cjs",
+  "scripts/changeset/lint.cjs",
+  "scripts/changeset/new.cjs",
+  "scripts/changeset/parse.cjs",
+  "scripts/changeset/render.cjs",
+  "scripts/changeset/serialize.cjs",
+  "scripts/fix-slash-commands.cjs",
+  "scripts/gen-capability-registry.cjs",
+  "scripts/gen-loop-host-contract.cjs",
+  "scripts/lib/allowlist-ratchet.cjs",
+  "scripts/lib/cli-exit.cjs",
+  "skills/gsd-add-tests/SKILL.md",
+  "skills/gsd-ai-integration-phase/SKILL.md",
+  "skills/gsd-audit-fix/SKILL.md",
+  "skills/gsd-audit-milestone/SKILL.md",
+  "skills/gsd-audit-uat/SKILL.md",
+  "skills/gsd-autonomous/SKILL.md",
+  "skills/gsd-capture/SKILL.md",
+  "skills/gsd-cleanup/SKILL.md",
+  "skills/gsd-code-review/SKILL.md",
+  "skills/gsd-complete-milestone/SKILL.md",
+  "skills/gsd-config/SKILL.md",
+  "skills/gsd-debug/SKILL.md",
+  "skills/gsd-discuss-phase/SKILL.md",
+  "skills/gsd-docs-update/SKILL.md",
+  "skills/gsd-eval-review/SKILL.md",
+  "skills/gsd-execute-phase/SKILL.md",
+  "skills/gsd-explore/SKILL.md",
+  "skills/gsd-extract-learnings/SKILL.md",
+  "skills/gsd-fast/SKILL.md",
+  "skills/gsd-forensics/SKILL.md",
+  "skills/gsd-graphify/SKILL.md",
+  "skills/gsd-health/SKILL.md",
+  "skills/gsd-help/SKILL.md",
+  "skills/gsd-import/SKILL.md",
+  "skills/gsd-inbox/SKILL.md",
+  "skills/gsd-ingest-docs/SKILL.md",
+  "skills/gsd-manager/SKILL.md",
+  "skills/gsd-map-codebase/SKILL.md",
+  "skills/gsd-mempalace-capture/SKILL.md",
+  "skills/gsd-mempalace-recall/SKILL.md",
+  "skills/gsd-milestone-summary/SKILL.md",
+  "skills/gsd-mvp-phase/SKILL.md",
+  "skills/gsd-new-milestone/SKILL.md",
+  "skills/gsd-new-project/SKILL.md",
+  "skills/gsd-next/SKILL.md",
+  "skills/gsd-ns-context/SKILL.md",
+  "skills/gsd-ns-ideate/SKILL.md",
+  "skills/gsd-ns-manage/SKILL.md",
+  "skills/gsd-ns-project/SKILL.md",
+  "skills/gsd-ns-review/SKILL.md",
+  "skills/gsd-ns-workflow/SKILL.md",
+  "skills/gsd-onboard/SKILL.md",
+  "skills/gsd-pause-work/SKILL.md",
+  "skills/gsd-phase/SKILL.md",
+  "skills/gsd-plan-phase/SKILL.md",
+  "skills/gsd-plan-review-convergence/SKILL.md",
+  "skills/gsd-pr-branch/SKILL.md",
+  "skills/gsd-profile-user/SKILL.md",
+  "skills/gsd-progress/SKILL.md",
+  "skills/gsd-quick/SKILL.md",
+  "skills/gsd-resume-work/SKILL.md",
+  "skills/gsd-review-backlog/SKILL.md",
+  "skills/gsd-review/SKILL.md",
+  "skills/gsd-secure-phase/SKILL.md",
+  "skills/gsd-settings/SKILL.md",
+  "skills/gsd-ship/SKILL.md",
+  "skills/gsd-sketch/SKILL.md",
+  "skills/gsd-spec-phase/SKILL.md",
+  "skills/gsd-spike/SKILL.md",
+  "skills/gsd-stats/SKILL.md",
+  "skills/gsd-surface/SKILL.md",
+  "skills/gsd-thread/SKILL.md",
+  "skills/gsd-ui-phase/SKILL.md",
+  "skills/gsd-ui-review/SKILL.md",
+  "skills/gsd-ultraplan-phase/SKILL.md",
+  "skills/gsd-undo/SKILL.md",
+  "skills/gsd-update/SKILL.md",
+  "skills/gsd-validate-phase/SKILL.md",
+  "skills/gsd-verify-work/SKILL.md",
+  "skills/gsd-workspace/SKILL.md",
+  "skills/gsd-workstreams/SKILL.md"
+]
diff --git a/tests/fixtures/install-tree/codex.json b/tests/fixtures/install-tree/codex.json
new file mode 100644
index 000000000..a5db2f467
--- /dev/null
+++ b/tests/fixtures/install-tree/codex.json
@@ -0,0 +1,435 @@
+[
+  ".agents/skills/gsd-add-tests/SKILL.md",
+  ".agents/skills/gsd-ai-integration-phase/SKILL.md",
+  ".agents/skills/gsd-audit-fix/SKILL.md",
+  ".agents/skills/gsd-audit-milestone/SKILL.md",
+  ".agents/skills/gsd-audit-uat/SKILL.md",
+  ".agents/skills/gsd-autonomous/SKILL.md",
+  ".agents/skills/gsd-capture/SKILL.md",
+  ".agents/skills/gsd-cleanup/SKILL.md",
+  ".agents/skills/gsd-code-review/SKILL.md",
+  ".agents/skills/gsd-complete-milestone/SKILL.md",
+  ".agents/skills/gsd-config/SKILL.md",
+  ".agents/skills/gsd-debug/SKILL.md",
+  ".agents/skills/gsd-discuss-phase/SKILL.md",
+  ".agents/skills/gsd-docs-update/SKILL.md",
+  ".agents/skills/gsd-eval-review/SKILL.md",
+  ".agents/skills/gsd-execute-phase/SKILL.md",
+  ".agents/skills/gsd-explore/SKILL.md",
+  ".agents/skills/gsd-extract-learnings/SKILL.md",
+  ".agents/skills/gsd-fast/SKILL.md",
+  ".agents/skills/gsd-forensics/SKILL.md",
+  ".agents/skills/gsd-graphify/SKILL.md",
+  ".agents/skills/gsd-health/SKILL.md",
+  ".agents/skills/gsd-help/SKILL.md",
+  ".agents/skills/gsd-import/SKILL.md",
+  ".agents/skills/gsd-inbox/SKILL.md",
+  ".agents/skills/gsd-ingest-docs/SKILL.md",
+  ".agents/skills/gsd-manager/SKILL.md",
+  ".agents/skills/gsd-map-codebase/SKILL.md",
+  ".agents/skills/gsd-mempalace-capture/SKILL.md",
+  ".agents/skills/gsd-mempalace-recall/SKILL.md",
+  ".agents/skills/gsd-milestone-summary/SKILL.md",
+  ".agents/skills/gsd-mvp-phase/SKILL.md",
+  ".agents/skills/gsd-new-milestone/SKILL.md",
+  ".agents/skills/gsd-new-project/SKILL.md",
+  ".agents/skills/gsd-next/SKILL.md",
+  ".agents/skills/gsd-ns-context/SKILL.md",
+  ".agents/skills/gsd-ns-ideate/SKILL.md",
+  ".agents/skills/gsd-ns-manage/SKILL.md",
+  ".agents/skills/gsd-ns-project/SKILL.md",
+  ".agents/skills/gsd-ns-review/SKILL.md",
+  ".agents/skills/gsd-ns-workflow/SKILL.md",
+  ".agents/skills/gsd-onboard/SKILL.md",
+  ".agents/skills/gsd-pause-work/SKILL.md",
+  ".agents/skills/gsd-phase/SKILL.md",
+  ".agents/skills/gsd-plan-phase/SKILL.md",
+  ".agents/skills/gsd-plan-review-convergence/SKILL.md",
+  ".agents/skills/gsd-pr-branch/SKILL.md",
+  ".agents/skills/gsd-profile-user/SKILL.md",
+  ".agents/skills/gsd-progress/SKILL.md",
+  ".agents/skills/gsd-quick/SKILL.md",
+  ".agents/skills/gsd-resume-work/SKILL.md",
+  ".agents/skills/gsd-review-backlog/SKILL.md",
+  ".agents/skills/gsd-review/SKILL.md",
+  ".agents/skills/gsd-secure-phase/SKILL.md",
+  ".agents/skills/gsd-settings/SKILL.md",
+  ".agents/skills/gsd-ship/SKILL.md",
+  ".agents/skills/gsd-sketch/SKILL.md",
+  ".agents/skills/gsd-spec-phase/SKILL.md",
+  ".agents/skills/gsd-spike/SKILL.md",
+  ".agents/skills/gsd-stats/SKILL.md",
+  ".agents/skills/gsd-surface/SKILL.md",
+  ".agents/skills/gsd-thread/SKILL.md",
+  ".agents/skills/gsd-ui-phase/SKILL.md",
+  ".agents/skills/gsd-ui-review/SKILL.md",
+  ".agents/skills/gsd-ultraplan-phase/SKILL.md",
+  ".agents/skills/gsd-undo/SKILL.md",
+  ".agents/skills/gsd-update/SKILL.md",
+  ".agents/skills/gsd-validate-phase/SKILL.md",
+  ".agents/skills/gsd-verify-work/SKILL.md",
+  ".agents/skills/gsd-workspace/SKILL.md",
+  ".agents/skills/gsd-workstreams/SKILL.md",
+  ".gsd-profile",
+  ".gsd/defaults.json",
+  "agents/gsd-advisor-researcher.md",
+  "agents/gsd-advisor-researcher.toml",
+  "agents/gsd-ai-researcher.md",
+  "agents/gsd-ai-researcher.toml",
+  "agents/gsd-assumptions-analyzer.md",
+  "agents/gsd-assumptions-analyzer.toml",
+  "agents/gsd-code-fixer.md",
+  "agents/gsd-code-fixer.toml",
+  "agents/gsd-code-reviewer.md",
+  "agents/gsd-code-reviewer.toml",
+  "agents/gsd-codebase-mapper.md",
+  "agents/gsd-codebase-mapper.toml",
+  "agents/gsd-debug-session-manager.md",
+  "agents/gsd-debug-session-manager.toml",
+  "agents/gsd-debugger.md",
+  "agents/gsd-debugger.toml",
+  "agents/gsd-doc-classifier.md",
+  "agents/gsd-doc-classifier.toml",
+  "agents/gsd-doc-synthesizer.md",
+  "agents/gsd-doc-synthesizer.toml",
+  "agents/gsd-doc-verifier.md",
+  "agents/gsd-doc-verifier.toml",
+  "agents/gsd-doc-writer.md",
+  "agents/gsd-doc-writer.toml",
+  "agents/gsd-domain-researcher.md",
+  "agents/gsd-domain-researcher.toml",
+  "agents/gsd-eval-auditor.md",
+  "agents/gsd-eval-auditor.toml",
+  "agents/gsd-eval-planner.md",
+  "agents/gsd-eval-planner.toml",
+  "agents/gsd-executor.md",
+  "agents/gsd-executor.toml",
+  "agents/gsd-framework-selector.md",
+  "agents/gsd-framework-selector.toml",
+  "agents/gsd-integration-checker.md",
+  "agents/gsd-integration-checker.toml",
+  "agents/gsd-intel-updater.md",
+  "agents/gsd-intel-updater.toml",
+  "agents/gsd-mempalace-curator.md",
+  "agents/gsd-mempalace-curator.toml",
+  "agents/gsd-nyquist-auditor.md",
+  "agents/gsd-nyquist-auditor.toml",
+  "agents/gsd-pattern-mapper.md",
+  "agents/gsd-pattern-mapper.toml",
+  "agents/gsd-phase-researcher.md",
+  "agents/gsd-phase-researcher.toml",
+  "agents/gsd-plan-checker.md",
+  "agents/gsd-plan-checker.toml",
+  "agents/gsd-planner.md",
+  "agents/gsd-planner.toml",
+  "agents/gsd-project-researcher.md",
+  "agents/gsd-project-researcher.toml",
+  "agents/gsd-research-synthesizer.md",
+  "agents/gsd-research-synthesizer.toml",
+  "agents/gsd-roadmapper.md",
+  "agents/gsd-roadmapper.toml",
+  "agents/gsd-security-auditor.md",
+  "agents/gsd-security-auditor.toml",
+  "agents/gsd-ui-auditor.md",
+  "agents/gsd-ui-auditor.toml",
+  "agents/gsd-ui-checker.md",
+  "agents/gsd-ui-checker.toml",
+  "agents/gsd-ui-researcher.md",
+  "agents/gsd-ui-researcher.toml",
+  "agents/gsd-user-profiler.md",
+  "agents/gsd-user-profiler.toml",
+  "agents/gsd-verifier.md",
+  "agents/gsd-verifier.toml",
+  "config.toml",
+  "gsd-core/VERSION",
+  "gsd-core/bin/check-latest-version.cjs",
+  "gsd-core/bin/ensure-runtime-build.cjs",
+  "gsd-core/bin/gsd-tools.cjs",
+  "gsd-core/bin/gsd_run",
+  "gsd-core/bin/shared/config-defaults.manifest.json",
+  "gsd-core/bin/shared/config-schema.manifest.json",
+  "gsd-core/bin/shared/model-catalog.json",
+  "gsd-core/bin/shared/runtime-aliases.manifest.json",
+  "gsd-core/bin/verify-reapply-patches.cjs",
+  "gsd-core/contexts/dev.md",
+  "gsd-core/contexts/research.md",
+  "gsd-core/contexts/review.md",
+  "gsd-core/references/agent-contracts.md",
+  "gsd-core/references/agent-skills-bootstrap.md",
+  "gsd-core/references/ai-evals.md",
+  "gsd-core/references/ai-frameworks.md",
+  "gsd-core/references/api-coverage.md",
+  "gsd-core/references/artifact-types.md",
+  "gsd-core/references/autonomous-smart-discuss.md",
+  "gsd-core/references/checkpoints.md",
+  "gsd-core/references/common-bug-patterns.md",
+  "gsd-core/references/context-budget.md",
+  "gsd-core/references/continuation-format.md",
+  "gsd-core/references/debugger-philosophy.md",
+  "gsd-core/references/decimal-phase-calculation.md",
+  "gsd-core/references/doc-conflict-engine.md",
+  "gsd-core/references/domain-probes.md",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/resolutions.json",
+  "gsd-core/references/edge-probe.md",
+  "gsd-core/references/execute-mvp-tdd.md",
+  "gsd-core/references/execute-phase-between-wave-reset.md",
+  "gsd-core/references/execute-phase-context-guard.md",
+  "gsd-core/references/execute-phase-wave-guard.md",
+  "gsd-core/references/executor-examples.md",
+  "gsd-core/references/few-shot-examples/plan-checker.md",
+  "gsd-core/references/few-shot-examples/verifier.md",
+  "gsd-core/references/gate-prompts.md",
+  "gsd-core/references/gates.md",
+  "gsd-core/references/git-integration.md",
+  "gsd-core/references/git-planning-commit.md",
+  "gsd-core/references/gsd-run-resolver.md",
+  "gsd-core/references/honest-verifier.md",
+  "gsd-core/references/ios-scaffold.md",
+  "gsd-core/references/loop-hook-dispatch.md",
+  "gsd-core/references/mandatory-initial-read.md",
+  "gsd-core/references/model-profile-resolution.md",
+  "gsd-core/references/model-profiles.md",
+  "gsd-core/references/mvp-concepts.md",
+  "gsd-core/references/phase-argument-parsing.md",
+  "gsd-core/references/planner-antipatterns.md",
+  "gsd-core/references/planner-chunked.md",
+  "gsd-core/references/planner-gap-closure.md",
+  "gsd-core/references/planner-graphify-auto-update.md",
+  "gsd-core/references/planner-guidance.md",
+  "gsd-core/references/planner-human-verify-mode.md",
+  "gsd-core/references/planner-interface-context.md",
+  "gsd-core/references/planner-load-graph-context.md",
+  "gsd-core/references/planner-mvp-mode.md",
+  "gsd-core/references/planner-reviews.md",
+  "gsd-core/references/planner-revision.md",
+  "gsd-core/references/planner-source-audit.md",
+  "gsd-core/references/planning-config.md",
+  "gsd-core/references/prohibition-probe-fixtures/01-streak-reminder/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/02-clean-utility/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/03-multi-prohibition/expected.json",
+  "gsd-core/references/prohibition-probe.md",
+  "gsd-core/references/project-skills-discovery.md",
+  "gsd-core/references/questioning.md",
+  "gsd-core/references/research-documentation-lookup.md",
+  "gsd-core/references/research-philosophy.md",
+  "gsd-core/references/research-verification-protocol.md",
+  "gsd-core/references/reviewer-instances.md",
+  "gsd-core/references/revision-loop.md",
+  "gsd-core/references/scout-codebase.md",
+  "gsd-core/references/security-asvs-levels.md",
+  "gsd-core/references/skeleton-template.md",
+  "gsd-core/references/sketch-interactivity.md",
+  "gsd-core/references/sketch-theme-system.md",
+  "gsd-core/references/sketch-tooling.md",
+  "gsd-core/references/sketch-variant-patterns.md",
+  "gsd-core/references/specless-probe-fallback.md",
+  "gsd-core/references/spidr-splitting.md",
+  "gsd-core/references/tdd.md",
+  "gsd-core/references/thinking-models-debug.md",
+  "gsd-core/references/thinking-models-execution.md",
+  "gsd-core/references/thinking-models-planning.md",
+  "gsd-core/references/thinking-models-research.md",
+  "gsd-core/references/thinking-models-verification.md",
+  "gsd-core/references/thinking-partner.md",
+  "gsd-core/references/ui-brand.md",
+  "gsd-core/references/ui-consideration-probe.md",
+  "gsd-core/references/universal-anti-patterns.md",
+  "gsd-core/references/untrusted-input-boundary.md",
+  "gsd-core/references/user-profiling.md",
+  "gsd-core/references/user-story-template.md",
+  "gsd-core/references/verification-overrides.md",
+  "gsd-core/references/verification-patterns.md",
+  "gsd-core/references/verify-mvp-mode.md",
+  "gsd-core/references/workstream-flag.md",
+  "gsd-core/references/worktree-branch-check.md",
+  "gsd-core/references/worktree-path-safety.md",
+  "gsd-core/templates/AI-SPEC.md",
+  "gsd-core/templates/DEBUG.md",
+  "gsd-core/templates/README.md",
+  "gsd-core/templates/SECURITY.md",
+  "gsd-core/templates/UAT.md",
+  "gsd-core/templates/UI-SPEC.md",
+  "gsd-core/templates/VALIDATION.md",
+  "gsd-core/templates/claude-md.md",
+  "gsd-core/templates/codebase/architecture.md",
+  "gsd-core/templates/codebase/concerns.md",
+  "gsd-core/templates/codebase/conventions.md",
+  "gsd-core/templates/codebase/integrations.md",
+  "gsd-core/templates/codebase/stack.md",
+  "gsd-core/templates/codebase/structure.md",
+  "gsd-core/templates/codebase/testing.md",
+  "gsd-core/templates/config.json",
+  "gsd-core/templates/context.md",
+  "gsd-core/templates/continue-here.md",
+  "gsd-core/templates/copilot-instructions.md",
+  "gsd-core/templates/debug-subagent-prompt.md",
+  "gsd-core/templates/dev-preferences.md",
+  "gsd-core/templates/discovery.md",
+  "gsd-core/templates/discussion-log.md",
+  "gsd-core/templates/milestone-archive.md",
+  "gsd-core/templates/milestone.md",
+  "gsd-core/templates/phase-prompt.md",
+  "gsd-core/templates/planner-subagent-prompt.md",
+  "gsd-core/templates/project.md",
+  "gsd-core/templates/requirements.md",
+  "gsd-core/templates/research-project/ARCHITECTURE.md",
+  "gsd-core/templates/research-project/FEATURES.md",
+  "gsd-core/templates/research-project/PITFALLS.md",
+  "gsd-core/templates/research-project/STACK.md",
+  "gsd-core/templates/research-project/SUMMARY.md",
+  "gsd-core/templates/research.md",
+  "gsd-core/templates/retrospective.md",
+  "gsd-core/templates/roadmap.md",
+  "gsd-core/templates/spec.md",
+  "gsd-core/templates/state.md",
+  "gsd-core/templates/summary-complex.md",
+  "gsd-core/templates/summary-minimal.md",
+  "gsd-core/templates/summary-standard.md",
+  "gsd-core/templates/summary.md",
+  "gsd-core/templates/user-profile.md",
+  "gsd-core/templates/user-setup.md",
+  "gsd-core/templates/verification-report.md",
+  "gsd-core/workflows/_runtime-launcher.snippet.sh",
+  "gsd-core/workflows/add-backlog.md",
+  "gsd-core/workflows/add-phase.md",
+  "gsd-core/workflows/add-tests.md",
+  "gsd-core/workflows/add-todo.md",
+  "gsd-core/workflows/ai-integration-phase.md",
+  "gsd-core/workflows/analyze-dependencies.md",
+  "gsd-core/workflows/audit-fix.md",
+  "gsd-core/workflows/audit-milestone.md",
+  "gsd-core/workflows/audit-uat.md",
+  "gsd-core/workflows/autonomous.md",
+  "gsd-core/workflows/check-todos.md",
+  "gsd-core/workflows/cleanup.md",
+  "gsd-core/workflows/code-review-fix.md",
+  "gsd-core/workflows/code-review.md",
+  "gsd-core/workflows/complete-milestone.md",
+  "gsd-core/workflows/debug.md",
+  "gsd-core/workflows/diagnose-issues.md",
+  "gsd-core/workflows/discovery-phase.md",
+  "gsd-core/workflows/discuss-phase-assumptions.md",
+  "gsd-core/workflows/discuss-phase-power.md",
+  "gsd-core/workflows/discuss-phase.md",
+  "gsd-core/workflows/discuss-phase/modes/advisor.md",
+  "gsd-core/workflows/discuss-phase/modes/all.md",
+  "gsd-core/workflows/discuss-phase/modes/analyze.md",
+  "gsd-core/workflows/discuss-phase/modes/auto.md",
+  "gsd-core/workflows/discuss-phase/modes/batch.md",
+  "gsd-core/workflows/discuss-phase/modes/chain.md",
+  "gsd-core/workflows/discuss-phase/modes/default.md",
+  "gsd-core/workflows/discuss-phase/modes/power.md",
+  "gsd-core/workflows/discuss-phase/modes/text.md",
+  "gsd-core/workflows/discuss-phase/templates/checkpoint.json",
+  "gsd-core/workflows/discuss-phase/templates/context.md",
+  "gsd-core/workflows/discuss-phase/templates/discussion-log.md",
+  "gsd-core/workflows/do.md",
+  "gsd-core/workflows/docs-update.md",
+  "gsd-core/workflows/edit-phase.md",
+  "gsd-core/workflows/eval-review.md",
+  "gsd-core/workflows/execute-phase.md",
+  "gsd-core/workflows/execute-phase/steps/codebase-drift-gate.md",
+  "gsd-core/workflows/execute-phase/steps/per-plan-worktree-gate.md",
+  "gsd-core/workflows/execute-phase/steps/post-merge-gate.md",
+  "gsd-core/workflows/execute-phase/steps/regression-gate.md",
+  "gsd-core/workflows/execute-phase/steps/worktree-recovery-policy.md",
+  "gsd-core/workflows/execute-plan.md",
+  "gsd-core/workflows/explore.md",
+  "gsd-core/workflows/extract-learnings.md",
+  "gsd-core/workflows/fast.md",
+  "gsd-core/workflows/forensics.md",
+  "gsd-core/workflows/graduation.md",
+  "gsd-core/workflows/health.md",
+  "gsd-core/workflows/help.md",
+  "gsd-core/workflows/help/modes/brief.md",
+  "gsd-core/workflows/help/modes/default.md",
+  "gsd-core/workflows/help/modes/full.md",
+  "gsd-core/workflows/help/modes/topic.md",
+  "gsd-core/workflows/import.md",
+  "gsd-core/workflows/inbox.md",
+  "gsd-core/workflows/ingest-docs.md",
+  "gsd-core/workflows/insert-phase.md",
+  "gsd-core/workflows/list-phase-assumptions.md",
+  "gsd-core/workflows/list-seeds.md",
+  "gsd-core/workflows/list-workspaces.md",
+  "gsd-core/workflows/manager.md",
+  "gsd-core/workflows/map-codebase.md",
+  "gsd-core/workflows/milestone-summary.md",
+  "gsd-core/workflows/mvp-phase.md",
+  "gsd-core/workflows/new-milestone.md",
+  "gsd-core/workflows/new-project.md",
+  "gsd-core/workflows/new-workspace.md",
+  "gsd-core/workflows/next.md",
+  "gsd-core/workflows/node-repair.md",
+  "gsd-core/workflows/note.md",
+  "gsd-core/workflows/onboard.md",
+  "gsd-core/workflows/pause-work.md",
+  "gsd-core/workflows/plan-milestone-gaps.md",
+  "gsd-core/workflows/plan-phase.md",
+  "gsd-core/workflows/plan-phase/steps/closed-phase-gate.md",
+  "gsd-core/workflows/plan-phase/steps/prd-express-path.md",
+  "gsd-core/workflows/plan-phase/steps/windows-troubleshooting.md",
+  "gsd-core/workflows/plan-review-convergence.md",
+  "gsd-core/workflows/plant-seed.md",
+  "gsd-core/workflows/pr-branch.md",
+  "gsd-core/workflows/profile-user.md",
+  "gsd-core/workflows/progress.md",
+  "gsd-core/workflows/quick.md",
+  "gsd-core/workflows/reapply-patches.md",
+  "gsd-core/workflows/remove-phase.md",
+  "gsd-core/workflows/remove-workspace.md",
+  "gsd-core/workflows/resume-project.md",
+  "gsd-core/workflows/review.md",
+  "gsd-core/workflows/scan.md",
+  "gsd-core/workflows/secure-phase.md",
+  "gsd-core/workflows/session-report.md",
+  "gsd-core/workflows/settings-advanced.md",
+  "gsd-core/workflows/settings-integrations.md",
+  "gsd-core/workflows/settings.md",
+  "gsd-core/workflows/ship.md",
+  "gsd-core/workflows/sketch-wrap-up.md",
+  "gsd-core/workflows/sketch.md",
+  "gsd-core/workflows/smart-entry.md",
+  "gsd-core/workflows/spec-phase.md",
+  "gsd-core/workflows/spike-wrap-up.md",
+  "gsd-core/workflows/spike.md",
+  "gsd-core/workflows/stats.md",
+  "gsd-core/workflows/sync-skills.md",
+  "gsd-core/workflows/thread.md",
+  "gsd-core/workflows/transition.md",
+  "gsd-core/workflows/ui-phase.md",
+  "gsd-core/workflows/ui-review.md",
+  "gsd-core/workflows/ultraplan-phase.md",
+  "gsd-core/workflows/undo.md",
+  "gsd-core/workflows/update.md",
+  "gsd-core/workflows/validate-phase.md",
+  "gsd-core/workflows/verify-phase.md",
+  "gsd-core/workflows/verify-work.md",
+  "hooks/gsd-check-update.js",
+  "hooks/gsd-context-monitor.js",
+  "scripts/changeset/README.md",
+  "scripts/changeset/cli.cjs",
+  "scripts/changeset/github-release-notes.cjs",
+  "scripts/changeset/lint.cjs",
+  "scripts/changeset/new.cjs",
+  "scripts/changeset/parse.cjs",
+  "scripts/changeset/render.cjs",
+  "scripts/changeset/serialize.cjs",
+  "scripts/fix-slash-commands.cjs",
+  "scripts/gen-capability-registry.cjs",
+  "scripts/gen-loop-host-contract.cjs",
+  "scripts/lib/allowlist-ratchet.cjs",
+  "scripts/lib/cli-exit.cjs"
+]
diff --git a/tests/fixtures/install-tree/copilot.json b/tests/fixtures/install-tree/copilot.json
new file mode 100644
index 000000000..bf257edbf
--- /dev/null
+++ b/tests/fixtures/install-tree/copilot.json
@@ -0,0 +1,400 @@
+[
+  ".gsd-profile",
+  ".gsd/defaults.json",
+  "agents/gsd-advisor-researcher.agent.md",
+  "agents/gsd-ai-researcher.agent.md",
+  "agents/gsd-assumptions-analyzer.agent.md",
+  "agents/gsd-code-fixer.agent.md",
+  "agents/gsd-code-reviewer.agent.md",
+  "agents/gsd-codebase-mapper.agent.md",
+  "agents/gsd-debug-session-manager.agent.md",
+  "agents/gsd-debugger.agent.md",
+  "agents/gsd-doc-classifier.agent.md",
+  "agents/gsd-doc-synthesizer.agent.md",
+  "agents/gsd-doc-verifier.agent.md",
+  "agents/gsd-doc-writer.agent.md",
+  "agents/gsd-domain-researcher.agent.md",
+  "agents/gsd-eval-auditor.agent.md",
+  "agents/gsd-eval-planner.agent.md",
+  "agents/gsd-executor.agent.md",
+  "agents/gsd-framework-selector.agent.md",
+  "agents/gsd-integration-checker.agent.md",
+  "agents/gsd-intel-updater.agent.md",
+  "agents/gsd-mempalace-curator.agent.md",
+  "agents/gsd-nyquist-auditor.agent.md",
+  "agents/gsd-pattern-mapper.agent.md",
+  "agents/gsd-phase-researcher.agent.md",
+  "agents/gsd-plan-checker.agent.md",
+  "agents/gsd-planner.agent.md",
+  "agents/gsd-project-researcher.agent.md",
+  "agents/gsd-research-synthesizer.agent.md",
+  "agents/gsd-roadmapper.agent.md",
+  "agents/gsd-security-auditor.agent.md",
+  "agents/gsd-ui-auditor.agent.md",
+  "agents/gsd-ui-checker.agent.md",
+  "agents/gsd-ui-researcher.agent.md",
+  "agents/gsd-user-profiler.agent.md",
+  "agents/gsd-verifier.agent.md",
+  "copilot-instructions.md",
+  "gsd-core/VERSION",
+  "gsd-core/bin/check-latest-version.cjs",
+  "gsd-core/bin/ensure-runtime-build.cjs",
+  "gsd-core/bin/gsd-tools.cjs",
+  "gsd-core/bin/gsd_run",
+  "gsd-core/bin/shared/config-defaults.manifest.json",
+  "gsd-core/bin/shared/config-schema.manifest.json",
+  "gsd-core/bin/shared/model-catalog.json",
+  "gsd-core/bin/shared/runtime-aliases.manifest.json",
+  "gsd-core/bin/verify-reapply-patches.cjs",
+  "gsd-core/contexts/dev.md",
+  "gsd-core/contexts/research.md",
+  "gsd-core/contexts/review.md",
+  "gsd-core/references/agent-contracts.md",
+  "gsd-core/references/agent-skills-bootstrap.md",
+  "gsd-core/references/ai-evals.md",
+  "gsd-core/references/ai-frameworks.md",
+  "gsd-core/references/api-coverage.md",
+  "gsd-core/references/artifact-types.md",
+  "gsd-core/references/autonomous-smart-discuss.md",
+  "gsd-core/references/checkpoints.md",
+  "gsd-core/references/common-bug-patterns.md",
+  "gsd-core/references/context-budget.md",
+  "gsd-core/references/continuation-format.md",
+  "gsd-core/references/debugger-philosophy.md",
+  "gsd-core/references/decimal-phase-calculation.md",
+  "gsd-core/references/doc-conflict-engine.md",
+  "gsd-core/references/domain-probes.md",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/resolutions.json",
+  "gsd-core/references/edge-probe.md",
+  "gsd-core/references/execute-mvp-tdd.md",
+  "gsd-core/references/execute-phase-between-wave-reset.md",
+  "gsd-core/references/execute-phase-context-guard.md",
+  "gsd-core/references/execute-phase-wave-guard.md",
+  "gsd-core/references/executor-examples.md",
+  "gsd-core/references/few-shot-examples/plan-checker.md",
+  "gsd-core/references/few-shot-examples/verifier.md",
+  "gsd-core/references/gate-prompts.md",
+  "gsd-core/references/gates.md",
+  "gsd-core/references/git-integration.md",
+  "gsd-core/references/git-planning-commit.md",
+  "gsd-core/references/gsd-run-resolver.md",
+  "gsd-core/references/honest-verifier.md",
+  "gsd-core/references/ios-scaffold.md",
+  "gsd-core/references/loop-hook-dispatch.md",
+  "gsd-core/references/mandatory-initial-read.md",
+  "gsd-core/references/model-profile-resolution.md",
+  "gsd-core/references/model-profiles.md",
+  "gsd-core/references/mvp-concepts.md",
+  "gsd-core/references/phase-argument-parsing.md",
+  "gsd-core/references/planner-antipatterns.md",
+  "gsd-core/references/planner-chunked.md",
+  "gsd-core/references/planner-gap-closure.md",
+  "gsd-core/references/planner-graphify-auto-update.md",
+  "gsd-core/references/planner-guidance.md",
+  "gsd-core/references/planner-human-verify-mode.md",
+  "gsd-core/references/planner-interface-context.md",
+  "gsd-core/references/planner-load-graph-context.md",
+  "gsd-core/references/planner-mvp-mode.md",
+  "gsd-core/references/planner-reviews.md",
+  "gsd-core/references/planner-revision.md",
+  "gsd-core/references/planner-source-audit.md",
+  "gsd-core/references/planning-config.md",
+  "gsd-core/references/prohibition-probe-fixtures/01-streak-reminder/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/02-clean-utility/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/03-multi-prohibition/expected.json",
+  "gsd-core/references/prohibition-probe.md",
+  "gsd-core/references/project-skills-discovery.md",
+  "gsd-core/references/questioning.md",
+  "gsd-core/references/research-documentation-lookup.md",
+  "gsd-core/references/research-philosophy.md",
+  "gsd-core/references/research-verification-protocol.md",
+  "gsd-core/references/reviewer-instances.md",
+  "gsd-core/references/revision-loop.md",
+  "gsd-core/references/scout-codebase.md",
+  "gsd-core/references/security-asvs-levels.md",
+  "gsd-core/references/skeleton-template.md",
+  "gsd-core/references/sketch-interactivity.md",
+  "gsd-core/references/sketch-theme-system.md",
+  "gsd-core/references/sketch-tooling.md",
+  "gsd-core/references/sketch-variant-patterns.md",
+  "gsd-core/references/specless-probe-fallback.md",
+  "gsd-core/references/spidr-splitting.md",
+  "gsd-core/references/tdd.md",
+  "gsd-core/references/thinking-models-debug.md",
+  "gsd-core/references/thinking-models-execution.md",
+  "gsd-core/references/thinking-models-planning.md",
+  "gsd-core/references/thinking-models-research.md",
+  "gsd-core/references/thinking-models-verification.md",
+  "gsd-core/references/thinking-partner.md",
+  "gsd-core/references/ui-brand.md",
+  "gsd-core/references/ui-consideration-probe.md",
+  "gsd-core/references/universal-anti-patterns.md",
+  "gsd-core/references/untrusted-input-boundary.md",
+  "gsd-core/references/user-profiling.md",
+  "gsd-core/references/user-story-template.md",
+  "gsd-core/references/verification-overrides.md",
+  "gsd-core/references/verification-patterns.md",
+  "gsd-core/references/verify-mvp-mode.md",
+  "gsd-core/references/workstream-flag.md",
+  "gsd-core/references/worktree-branch-check.md",
+  "gsd-core/references/worktree-path-safety.md",
+  "gsd-core/templates/AI-SPEC.md",
+  "gsd-core/templates/DEBUG.md",
+  "gsd-core/templates/README.md",
+  "gsd-core/templates/SECURITY.md",
+  "gsd-core/templates/UAT.md",
+  "gsd-core/templates/UI-SPEC.md",
+  "gsd-core/templates/VALIDATION.md",
+  "gsd-core/templates/claude-md.md",
+  "gsd-core/templates/codebase/architecture.md",
+  "gsd-core/templates/codebase/concerns.md",
+  "gsd-core/templates/codebase/conventions.md",
+  "gsd-core/templates/codebase/integrations.md",
+  "gsd-core/templates/codebase/stack.md",
+  "gsd-core/templates/codebase/structure.md",
+  "gsd-core/templates/codebase/testing.md",
+  "gsd-core/templates/config.json",
+  "gsd-core/templates/context.md",
+  "gsd-core/templates/continue-here.md",
+  "gsd-core/templates/copilot-instructions.md",
+  "gsd-core/templates/debug-subagent-prompt.md",
+  "gsd-core/templates/dev-preferences.md",
+  "gsd-core/templates/discovery.md",
+  "gsd-core/templates/discussion-log.md",
+  "gsd-core/templates/milestone-archive.md",
+  "gsd-core/templates/milestone.md",
+  "gsd-core/templates/phase-prompt.md",
+  "gsd-core/templates/planner-subagent-prompt.md",
+  "gsd-core/templates/project.md",
+  "gsd-core/templates/requirements.md",
+  "gsd-core/templates/research-project/ARCHITECTURE.md",
+  "gsd-core/templates/research-project/FEATURES.md",
+  "gsd-core/templates/research-project/PITFALLS.md",
+  "gsd-core/templates/research-project/STACK.md",
+  "gsd-core/templates/research-project/SUMMARY.md",
+  "gsd-core/templates/research.md",
+  "gsd-core/templates/retrospective.md",
+  "gsd-core/templates/roadmap.md",
+  "gsd-core/templates/spec.md",
+  "gsd-core/templates/state.md",
+  "gsd-core/templates/summary-complex.md",
+  "gsd-core/templates/summary-minimal.md",
+  "gsd-core/templates/summary-standard.md",
+  "gsd-core/templates/summary.md",
+  "gsd-core/templates/user-profile.md",
+  "gsd-core/templates/user-setup.md",
+  "gsd-core/templates/verification-report.md",
+  "gsd-core/workflows/_runtime-launcher.snippet.sh",
+  "gsd-core/workflows/add-backlog.md",
+  "gsd-core/workflows/add-phase.md",
+  "gsd-core/workflows/add-tests.md",
+  "gsd-core/workflows/add-todo.md",
+  "gsd-core/workflows/ai-integration-phase.md",
+  "gsd-core/workflows/analyze-dependencies.md",
+  "gsd-core/workflows/audit-fix.md",
+  "gsd-core/workflows/audit-milestone.md",
+  "gsd-core/workflows/audit-uat.md",
+  "gsd-core/workflows/autonomous.md",
+  "gsd-core/workflows/check-todos.md",
+  "gsd-core/workflows/cleanup.md",
+  "gsd-core/workflows/code-review-fix.md",
+  "gsd-core/workflows/code-review.md",
+  "gsd-core/workflows/complete-milestone.md",
+  "gsd-core/workflows/debug.md",
+  "gsd-core/workflows/diagnose-issues.md",
+  "gsd-core/workflows/discovery-phase.md",
+  "gsd-core/workflows/discuss-phase-assumptions.md",
+  "gsd-core/workflows/discuss-phase-power.md",
+  "gsd-core/workflows/discuss-phase.md",
+  "gsd-core/workflows/discuss-phase/modes/advisor.md",
+  "gsd-core/workflows/discuss-phase/modes/all.md",
+  "gsd-core/workflows/discuss-phase/modes/analyze.md",
+  "gsd-core/workflows/discuss-phase/modes/auto.md",
+  "gsd-core/workflows/discuss-phase/modes/batch.md",
+  "gsd-core/workflows/discuss-phase/modes/chain.md",
+  "gsd-core/workflows/discuss-phase/modes/default.md",
+  "gsd-core/workflows/discuss-phase/modes/power.md",
+  "gsd-core/workflows/discuss-phase/modes/text.md",
+  "gsd-core/workflows/discuss-phase/templates/checkpoint.json",
+  "gsd-core/workflows/discuss-phase/templates/context.md",
+  "gsd-core/workflows/discuss-phase/templates/discussion-log.md",
+  "gsd-core/workflows/do.md",
+  "gsd-core/workflows/docs-update.md",
+  "gsd-core/workflows/edit-phase.md",
+  "gsd-core/workflows/eval-review.md",
+  "gsd-core/workflows/execute-phase.md",
+  "gsd-core/workflows/execute-phase/steps/codebase-drift-gate.md",
+  "gsd-core/workflows/execute-phase/steps/per-plan-worktree-gate.md",
+  "gsd-core/workflows/execute-phase/steps/post-merge-gate.md",
+  "gsd-core/workflows/execute-phase/steps/regression-gate.md",
+  "gsd-core/workflows/execute-phase/steps/worktree-recovery-policy.md",
+  "gsd-core/workflows/execute-plan.md",
+  "gsd-core/workflows/explore.md",
+  "gsd-core/workflows/extract-learnings.md",
+  "gsd-core/workflows/fast.md",
+  "gsd-core/workflows/forensics.md",
+  "gsd-core/workflows/graduation.md",
+  "gsd-core/workflows/health.md",
+  "gsd-core/workflows/help.md",
+  "gsd-core/workflows/help/modes/brief.md",
+  "gsd-core/workflows/help/modes/default.md",
+  "gsd-core/workflows/help/modes/full.md",
+  "gsd-core/workflows/help/modes/topic.md",
+  "gsd-core/workflows/import.md",
+  "gsd-core/workflows/inbox.md",
+  "gsd-core/workflows/ingest-docs.md",
+  "gsd-core/workflows/insert-phase.md",
+  "gsd-core/workflows/list-phase-assumptions.md",
+  "gsd-core/workflows/list-seeds.md",
+  "gsd-core/workflows/list-workspaces.md",
+  "gsd-core/workflows/manager.md",
+  "gsd-core/workflows/map-codebase.md",
+  "gsd-core/workflows/milestone-summary.md",
+  "gsd-core/workflows/mvp-phase.md",
+  "gsd-core/workflows/new-milestone.md",
+  "gsd-core/workflows/new-project.md",
+  "gsd-core/workflows/new-workspace.md",
+  "gsd-core/workflows/next.md",
+  "gsd-core/workflows/node-repair.md",
+  "gsd-core/workflows/note.md",
+  "gsd-core/workflows/onboard.md",
+  "gsd-core/workflows/pause-work.md",
+  "gsd-core/workflows/plan-milestone-gaps.md",
+  "gsd-core/workflows/plan-phase.md",
+  "gsd-core/workflows/plan-phase/steps/closed-phase-gate.md",
+  "gsd-core/workflows/plan-phase/steps/prd-express-path.md",
+  "gsd-core/workflows/plan-phase/steps/windows-troubleshooting.md",
+  "gsd-core/workflows/plan-review-convergence.md",
+  "gsd-core/workflows/plant-seed.md",
+  "gsd-core/workflows/pr-branch.md",
+  "gsd-core/workflows/profile-user.md",
+  "gsd-core/workflows/progress.md",
+  "gsd-core/workflows/quick.md",
+  "gsd-core/workflows/reapply-patches.md",
+  "gsd-core/workflows/remove-phase.md",
+  "gsd-core/workflows/remove-workspace.md",
+  "gsd-core/workflows/resume-project.md",
+  "gsd-core/workflows/review.md",
+  "gsd-core/workflows/scan.md",
+  "gsd-core/workflows/secure-phase.md",
+  "gsd-core/workflows/session-report.md",
+  "gsd-core/workflows/settings-advanced.md",
+  "gsd-core/workflows/settings-integrations.md",
+  "gsd-core/workflows/settings.md",
+  "gsd-core/workflows/ship.md",
+  "gsd-core/workflows/sketch-wrap-up.md",
+  "gsd-core/workflows/sketch.md",
+  "gsd-core/workflows/smart-entry.md",
+  "gsd-core/workflows/spec-phase.md",
+  "gsd-core/workflows/spike-wrap-up.md",
+  "gsd-core/workflows/spike.md",
+  "gsd-core/workflows/stats.md",
+  "gsd-core/workflows/sync-skills.md",
+  "gsd-core/workflows/thread.md",
+  "gsd-core/workflows/transition.md",
+  "gsd-core/workflows/ui-phase.md",
+  "gsd-core/workflows/ui-review.md",
+  "gsd-core/workflows/ultraplan-phase.md",
+  "gsd-core/workflows/undo.md",
+  "gsd-core/workflows/update.md",
+  "gsd-core/workflows/validate-phase.md",
+  "gsd-core/workflows/verify-phase.md",
+  "gsd-core/workflows/verify-work.md",
+  "hooks/gsd-session.json",
+  "scripts/changeset/README.md",
+  "scripts/changeset/cli.cjs",
+  "scripts/changeset/github-release-notes.cjs",
+  "scripts/changeset/lint.cjs",
+  "scripts/changeset/new.cjs",
+  "scripts/changeset/parse.cjs",
+  "scripts/changeset/render.cjs",
+  "scripts/changeset/serialize.cjs",
+  "scripts/fix-slash-commands.cjs",
+  "scripts/gen-capability-registry.cjs",
+  "scripts/gen-loop-host-contract.cjs",
+  "scripts/lib/allowlist-ratchet.cjs",
+  "scripts/lib/cli-exit.cjs",
+  "skills/gsd-add-tests/SKILL.md",
+  "skills/gsd-ai-integration-phase/SKILL.md",
+  "skills/gsd-audit-fix/SKILL.md",
+  "skills/gsd-audit-milestone/SKILL.md",
+  "skills/gsd-audit-uat/SKILL.md",
+  "skills/gsd-autonomous/SKILL.md",
+  "skills/gsd-capture/SKILL.md",
+  "skills/gsd-cleanup/SKILL.md",
+  "skills/gsd-code-review/SKILL.md",
+  "skills/gsd-complete-milestone/SKILL.md",
+  "skills/gsd-config/SKILL.md",
+  "skills/gsd-debug/SKILL.md",
+  "skills/gsd-discuss-phase/SKILL.md",
+  "skills/gsd-docs-update/SKILL.md",
+  "skills/gsd-eval-review/SKILL.md",
+  "skills/gsd-execute-phase/SKILL.md",
+  "skills/gsd-explore/SKILL.md",
+  "skills/gsd-extract-learnings/SKILL.md",
+  "skills/gsd-fast/SKILL.md",
+  "skills/gsd-forensics/SKILL.md",
+  "skills/gsd-graphify/SKILL.md",
+  "skills/gsd-health/SKILL.md",
+  "skills/gsd-help/SKILL.md",
+  "skills/gsd-import/SKILL.md",
+  "skills/gsd-inbox/SKILL.md",
+  "skills/gsd-ingest-docs/SKILL.md",
+  "skills/gsd-manager/SKILL.md",
+  "skills/gsd-map-codebase/SKILL.md",
+  "skills/gsd-mempalace-capture/SKILL.md",
+  "skills/gsd-mempalace-recall/SKILL.md",
+  "skills/gsd-milestone-summary/SKILL.md",
+  "skills/gsd-mvp-phase/SKILL.md",
+  "skills/gsd-new-milestone/SKILL.md",
+  "skills/gsd-new-project/SKILL.md",
+  "skills/gsd-next/SKILL.md",
+  "skills/gsd-ns-context/SKILL.md",
+  "skills/gsd-ns-ideate/SKILL.md",
+  "skills/gsd-ns-manage/SKILL.md",
+  "skills/gsd-ns-project/SKILL.md",
+  "skills/gsd-ns-review/SKILL.md",
+  "skills/gsd-ns-workflow/SKILL.md",
+  "skills/gsd-onboard/SKILL.md",
+  "skills/gsd-pause-work/SKILL.md",
+  "skills/gsd-phase/SKILL.md",
+  "skills/gsd-plan-phase/SKILL.md",
+  "skills/gsd-plan-review-convergence/SKILL.md",
+  "skills/gsd-pr-branch/SKILL.md",
+  "skills/gsd-profile-user/SKILL.md",
+  "skills/gsd-progress/SKILL.md",
+  "skills/gsd-quick/SKILL.md",
+  "skills/gsd-resume-work/SKILL.md",
+  "skills/gsd-review-backlog/SKILL.md",
+  "skills/gsd-review/SKILL.md",
+  "skills/gsd-secure-phase/SKILL.md",
+  "skills/gsd-settings/SKILL.md",
+  "skills/gsd-ship/SKILL.md",
+  "skills/gsd-sketch/SKILL.md",
+  "skills/gsd-spec-phase/SKILL.md",
+  "skills/gsd-spike/SKILL.md",
+  "skills/gsd-stats/SKILL.md",
+  "skills/gsd-surface/SKILL.md",
+  "skills/gsd-thread/SKILL.md",
+  "skills/gsd-ui-phase/SKILL.md",
+  "skills/gsd-ui-review/SKILL.md",
+  "skills/gsd-ultraplan-phase/SKILL.md",
+  "skills/gsd-undo/SKILL.md",
+  "skills/gsd-update/SKILL.md",
+  "skills/gsd-validate-phase/SKILL.md",
+  "skills/gsd-verify-work/SKILL.md",
+  "skills/gsd-workspace/SKILL.md",
+  "skills/gsd-workstreams/SKILL.md"
+]
diff --git a/tests/fixtures/install-tree/cursor.json b/tests/fixtures/install-tree/cursor.json
new file mode 100644
index 000000000..373692429
--- /dev/null
+++ b/tests/fixtures/install-tree/cursor.json
@@ -0,0 +1,475 @@
+[
+  ".gsd-profile",
+  ".gsd/defaults.json",
+  "agents/gsd-advisor-researcher.md",
+  "agents/gsd-ai-researcher.md",
+  "agents/gsd-assumptions-analyzer.md",
+  "agents/gsd-code-fixer.md",
+  "agents/gsd-code-reviewer.md",
+  "agents/gsd-codebase-mapper.md",
+  "agents/gsd-debug-session-manager.md",
+  "agents/gsd-debugger.md",
+  "agents/gsd-doc-classifier.md",
+  "agents/gsd-doc-synthesizer.md",
+  "agents/gsd-doc-verifier.md",
+  "agents/gsd-doc-writer.md",
+  "agents/gsd-domain-researcher.md",
+  "agents/gsd-eval-auditor.md",
+  "agents/gsd-eval-planner.md",
+  "agents/gsd-executor.md",
+  "agents/gsd-framework-selector.md",
+  "agents/gsd-integration-checker.md",
+  "agents/gsd-intel-updater.md",
+  "agents/gsd-mempalace-curator.md",
+  "agents/gsd-nyquist-auditor.md",
+  "agents/gsd-pattern-mapper.md",
+  "agents/gsd-phase-researcher.md",
+  "agents/gsd-plan-checker.md",
+  "agents/gsd-planner.md",
+  "agents/gsd-project-researcher.md",
+  "agents/gsd-research-synthesizer.md",
+  "agents/gsd-roadmapper.md",
+  "agents/gsd-security-auditor.md",
+  "agents/gsd-ui-auditor.md",
+  "agents/gsd-ui-checker.md",
+  "agents/gsd-ui-researcher.md",
+  "agents/gsd-user-profiler.md",
+  "agents/gsd-verifier.md",
+  "commands/gsd-add-tests.md",
+  "commands/gsd-ai-integration-phase.md",
+  "commands/gsd-audit-fix.md",
+  "commands/gsd-audit-milestone.md",
+  "commands/gsd-audit-uat.md",
+  "commands/gsd-autonomous.md",
+  "commands/gsd-capture.md",
+  "commands/gsd-cleanup.md",
+  "commands/gsd-code-review.md",
+  "commands/gsd-complete-milestone.md",
+  "commands/gsd-config.md",
+  "commands/gsd-debug.md",
+  "commands/gsd-discuss-phase.md",
+  "commands/gsd-docs-update.md",
+  "commands/gsd-eval-review.md",
+  "commands/gsd-execute-phase.md",
+  "commands/gsd-explore.md",
+  "commands/gsd-extract-learnings.md",
+  "commands/gsd-fast.md",
+  "commands/gsd-forensics.md",
+  "commands/gsd-graphify.md",
+  "commands/gsd-health.md",
+  "commands/gsd-help.md",
+  "commands/gsd-import.md",
+  "commands/gsd-inbox.md",
+  "commands/gsd-ingest-docs.md",
+  "commands/gsd-manager.md",
+  "commands/gsd-map-codebase.md",
+  "commands/gsd-mempalace-capture.md",
+  "commands/gsd-mempalace-recall.md",
+  "commands/gsd-milestone-summary.md",
+  "commands/gsd-mvp-phase.md",
+  "commands/gsd-new-milestone.md",
+  "commands/gsd-new-project.md",
+  "commands/gsd-next.md",
+  "commands/gsd-ns-context.md",
+  "commands/gsd-ns-ideate.md",
+  "commands/gsd-ns-manage.md",
+  "commands/gsd-ns-project.md",
+  "commands/gsd-ns-review.md",
+  "commands/gsd-ns-workflow.md",
+  "commands/gsd-onboard.md",
+  "commands/gsd-pause-work.md",
+  "commands/gsd-phase.md",
+  "commands/gsd-plan-phase.md",
+  "commands/gsd-plan-review-convergence.md",
+  "commands/gsd-pr-branch.md",
+  "commands/gsd-profile-user.md",
+  "commands/gsd-progress.md",
+  "commands/gsd-quick.md",
+  "commands/gsd-resume-work.md",
+  "commands/gsd-review-backlog.md",
+  "commands/gsd-review.md",
+  "commands/gsd-secure-phase.md",
+  "commands/gsd-settings.md",
+  "commands/gsd-ship.md",
+  "commands/gsd-sketch.md",
+  "commands/gsd-spec-phase.md",
+  "commands/gsd-spike.md",
+  "commands/gsd-stats.md",
+  "commands/gsd-surface.md",
+  "commands/gsd-thread.md",
+  "commands/gsd-ui-phase.md",
+  "commands/gsd-ui-review.md",
+  "commands/gsd-ultraplan-phase.md",
+  "commands/gsd-undo.md",
+  "commands/gsd-update.md",
+  "commands/gsd-validate-phase.md",
+  "commands/gsd-verify-work.md",
+  "commands/gsd-workspace.md",
+  "commands/gsd-workstreams.md",
+  "gsd-core/VERSION",
+  "gsd-core/bin/check-latest-version.cjs",
+  "gsd-core/bin/ensure-runtime-build.cjs",
+  "gsd-core/bin/gsd-tools.cjs",
+  "gsd-core/bin/gsd_run",
+  "gsd-core/bin/shared/config-defaults.manifest.json",
+  "gsd-core/bin/shared/config-schema.manifest.json",
+  "gsd-core/bin/shared/model-catalog.json",
+  "gsd-core/bin/shared/runtime-aliases.manifest.json",
+  "gsd-core/bin/verify-reapply-patches.cjs",
+  "gsd-core/contexts/dev.md",
+  "gsd-core/contexts/research.md",
+  "gsd-core/contexts/review.md",
+  "gsd-core/references/agent-contracts.md",
+  "gsd-core/references/agent-skills-bootstrap.md",
+  "gsd-core/references/ai-evals.md",
+  "gsd-core/references/ai-frameworks.md",
+  "gsd-core/references/api-coverage.md",
+  "gsd-core/references/artifact-types.md",
+  "gsd-core/references/autonomous-smart-discuss.md",
+  "gsd-core/references/checkpoints.md",
+  "gsd-core/references/common-bug-patterns.md",
+  "gsd-core/references/context-budget.md",
+  "gsd-core/references/continuation-format.md",
+  "gsd-core/references/debugger-philosophy.md",
+  "gsd-core/references/decimal-phase-calculation.md",
+  "gsd-core/references/doc-conflict-engine.md",
+  "gsd-core/references/domain-probes.md",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/resolutions.json",
+  "gsd-core/references/edge-probe.md",
+  "gsd-core/references/execute-mvp-tdd.md",
+  "gsd-core/references/execute-phase-between-wave-reset.md",
+  "gsd-core/references/execute-phase-context-guard.md",
+  "gsd-core/references/execute-phase-wave-guard.md",
+  "gsd-core/references/executor-examples.md",
+  "gsd-core/references/few-shot-examples/plan-checker.md",
+  "gsd-core/references/few-shot-examples/verifier.md",
+  "gsd-core/references/gate-prompts.md",
+  "gsd-core/references/gates.md",
+  "gsd-core/references/git-integration.md",
+  "gsd-core/references/git-planning-commit.md",
+  "gsd-core/references/gsd-run-resolver.md",
+  "gsd-core/references/honest-verifier.md",
+  "gsd-core/references/ios-scaffold.md",
+  "gsd-core/references/loop-hook-dispatch.md",
+  "gsd-core/references/mandatory-initial-read.md",
+  "gsd-core/references/model-profile-resolution.md",
+  "gsd-core/references/model-profiles.md",
+  "gsd-core/references/mvp-concepts.md",
+  "gsd-core/references/phase-argument-parsing.md",
+  "gsd-core/references/planner-antipatterns.md",
+  "gsd-core/references/planner-chunked.md",
+  "gsd-core/references/planner-gap-closure.md",
+  "gsd-core/references/planner-graphify-auto-update.md",
+  "gsd-core/references/planner-guidance.md",
+  "gsd-core/references/planner-human-verify-mode.md",
+  "gsd-core/references/planner-interface-context.md",
+  "gsd-core/references/planner-load-graph-context.md",
+  "gsd-core/references/planner-mvp-mode.md",
+  "gsd-core/references/planner-reviews.md",
+  "gsd-core/references/planner-revision.md",
+  "gsd-core/references/planner-source-audit.md",
+  "gsd-core/references/planning-config.md",
+  "gsd-core/references/prohibition-probe-fixtures/01-streak-reminder/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/02-clean-utility/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/03-multi-prohibition/expected.json",
+  "gsd-core/references/prohibition-probe.md",
+  "gsd-core/references/project-skills-discovery.md",
+  "gsd-core/references/questioning.md",
+  "gsd-core/references/research-documentation-lookup.md",
+  "gsd-core/references/research-philosophy.md",
+  "gsd-core/references/research-verification-protocol.md",
+  "gsd-core/references/reviewer-instances.md",
+  "gsd-core/references/revision-loop.md",
+  "gsd-core/references/scout-codebase.md",
+  "gsd-core/references/security-asvs-levels.md",
+  "gsd-core/references/skeleton-template.md",
+  "gsd-core/references/sketch-interactivity.md",
+  "gsd-core/references/sketch-theme-system.md",
+  "gsd-core/references/sketch-tooling.md",
+  "gsd-core/references/sketch-variant-patterns.md",
+  "gsd-core/references/specless-probe-fallback.md",
+  "gsd-core/references/spidr-splitting.md",
+  "gsd-core/references/tdd.md",
+  "gsd-core/references/thinking-models-debug.md",
+  "gsd-core/references/thinking-models-execution.md",
+  "gsd-core/references/thinking-models-planning.md",
+  "gsd-core/references/thinking-models-research.md",
+  "gsd-core/references/thinking-models-verification.md",
+  "gsd-core/references/thinking-partner.md",
+  "gsd-core/references/ui-brand.md",
+  "gsd-core/references/ui-consideration-probe.md",
+  "gsd-core/references/universal-anti-patterns.md",
+  "gsd-core/references/untrusted-input-boundary.md",
+  "gsd-core/references/user-profiling.md",
+  "gsd-core/references/user-story-template.md",
+  "gsd-core/references/verification-overrides.md",
+  "gsd-core/references/verification-patterns.md",
+  "gsd-core/references/verify-mvp-mode.md",
+  "gsd-core/references/workstream-flag.md",
+  "gsd-core/references/worktree-branch-check.md",
+  "gsd-core/references/worktree-path-safety.md",
+  "gsd-core/templates/AI-SPEC.md",
+  "gsd-core/templates/DEBUG.md",
+  "gsd-core/templates/README.md",
+  "gsd-core/templates/SECURITY.md",
+  "gsd-core/templates/UAT.md",
+  "gsd-core/templates/UI-SPEC.md",
+  "gsd-core/templates/VALIDATION.md",
+  "gsd-core/templates/claude-md.md",
+  "gsd-core/templates/codebase/architecture.md",
+  "gsd-core/templates/codebase/concerns.md",
+  "gsd-core/templates/codebase/conventions.md",
+  "gsd-core/templates/codebase/integrations.md",
+  "gsd-core/templates/codebase/stack.md",
+  "gsd-core/templates/codebase/structure.md",
+  "gsd-core/templates/codebase/testing.md",
+  "gsd-core/templates/config.json",
+  "gsd-core/templates/context.md",
+  "gsd-core/templates/continue-here.md",
+  "gsd-core/templates/copilot-instructions.md",
+  "gsd-core/templates/debug-subagent-prompt.md",
+  "gsd-core/templates/dev-preferences.md",
+  "gsd-core/templates/discovery.md",
+  "gsd-core/templates/discussion-log.md",
+  "gsd-core/templates/milestone-archive.md",
+  "gsd-core/templates/milestone.md",
+  "gsd-core/templates/phase-prompt.md",
+  "gsd-core/templates/planner-subagent-prompt.md",
+  "gsd-core/templates/project.md",
+  "gsd-core/templates/requirements.md",
+  "gsd-core/templates/research-project/ARCHITECTURE.md",
+  "gsd-core/templates/research-project/FEATURES.md",
+  "gsd-core/templates/research-project/PITFALLS.md",
+  "gsd-core/templates/research-project/STACK.md",
+  "gsd-core/templates/research-project/SUMMARY.md",
+  "gsd-core/templates/research.md",
+  "gsd-core/templates/retrospective.md",
+  "gsd-core/templates/roadmap.md",
+  "gsd-core/templates/spec.md",
+  "gsd-core/templates/state.md",
+  "gsd-core/templates/summary-complex.md",
+  "gsd-core/templates/summary-minimal.md",
+  "gsd-core/templates/summary-standard.md",
+  "gsd-core/templates/summary.md",
+  "gsd-core/templates/user-profile.md",
+  "gsd-core/templates/user-setup.md",
+  "gsd-core/templates/verification-report.md",
+  "gsd-core/workflows/_runtime-launcher.snippet.sh",
+  "gsd-core/workflows/add-backlog.md",
+  "gsd-core/workflows/add-phase.md",
+  "gsd-core/workflows/add-tests.md",
+  "gsd-core/workflows/add-todo.md",
+  "gsd-core/workflows/ai-integration-phase.md",
+  "gsd-core/workflows/analyze-dependencies.md",
+  "gsd-core/workflows/audit-fix.md",
+  "gsd-core/workflows/audit-milestone.md",
+  "gsd-core/workflows/audit-uat.md",
+  "gsd-core/workflows/autonomous.md",
+  "gsd-core/workflows/check-todos.md",
+  "gsd-core/workflows/cleanup.md",
+  "gsd-core/workflows/code-review-fix.md",
+  "gsd-core/workflows/code-review.md",
+  "gsd-core/workflows/complete-milestone.md",
+  "gsd-core/workflows/debug.md",
+  "gsd-core/workflows/diagnose-issues.md",
+  "gsd-core/workflows/discovery-phase.md",
+  "gsd-core/workflows/discuss-phase-assumptions.md",
+  "gsd-core/workflows/discuss-phase-power.md",
+  "gsd-core/workflows/discuss-phase.md",
+  "gsd-core/workflows/discuss-phase/modes/advisor.md",
+  "gsd-core/workflows/discuss-phase/modes/all.md",
+  "gsd-core/workflows/discuss-phase/modes/analyze.md",
+  "gsd-core/workflows/discuss-phase/modes/auto.md",
+  "gsd-core/workflows/discuss-phase/modes/batch.md",
+  "gsd-core/workflows/discuss-phase/modes/chain.md",
+  "gsd-core/workflows/discuss-phase/modes/default.md",
+  "gsd-core/workflows/discuss-phase/modes/power.md",
+  "gsd-core/workflows/discuss-phase/modes/text.md",
+  "gsd-core/workflows/discuss-phase/templates/checkpoint.json",
+  "gsd-core/workflows/discuss-phase/templates/context.md",
+  "gsd-core/workflows/discuss-phase/templates/discussion-log.md",
+  "gsd-core/workflows/do.md",
+  "gsd-core/workflows/docs-update.md",
+  "gsd-core/workflows/edit-phase.md",
+  "gsd-core/workflows/eval-review.md",
+  "gsd-core/workflows/execute-phase.md",
+  "gsd-core/workflows/execute-phase/steps/codebase-drift-gate.md",
+  "gsd-core/workflows/execute-phase/steps/per-plan-worktree-gate.md",
+  "gsd-core/workflows/execute-phase/steps/post-merge-gate.md",
+  "gsd-core/workflows/execute-phase/steps/regression-gate.md",
+  "gsd-core/workflows/execute-phase/steps/worktree-recovery-policy.md",
+  "gsd-core/workflows/execute-plan.md",
+  "gsd-core/workflows/explore.md",
+  "gsd-core/workflows/extract-learnings.md",
+  "gsd-core/workflows/fast.md",
+  "gsd-core/workflows/forensics.md",
+  "gsd-core/workflows/graduation.md",
+  "gsd-core/workflows/health.md",
+  "gsd-core/workflows/help.md",
+  "gsd-core/workflows/help/modes/brief.md",
+  "gsd-core/workflows/help/modes/default.md",
+  "gsd-core/workflows/help/modes/full.md",
+  "gsd-core/workflows/help/modes/topic.md",
+  "gsd-core/workflows/import.md",
+  "gsd-core/workflows/inbox.md",
+  "gsd-core/workflows/ingest-docs.md",
+  "gsd-core/workflows/insert-phase.md",
+  "gsd-core/workflows/list-phase-assumptions.md",
+  "gsd-core/workflows/list-seeds.md",
+  "gsd-core/workflows/list-workspaces.md",
+  "gsd-core/workflows/manager.md",
+  "gsd-core/workflows/map-codebase.md",
+  "gsd-core/workflows/milestone-summary.md",
+  "gsd-core/workflows/mvp-phase.md",
+  "gsd-core/workflows/new-milestone.md",
+  "gsd-core/workflows/new-project.md",
+  "gsd-core/workflows/new-workspace.md",
+  "gsd-core/workflows/next.md",
+  "gsd-core/workflows/node-repair.md",
+  "gsd-core/workflows/note.md",
+  "gsd-core/workflows/onboard.md",
+  "gsd-core/workflows/pause-work.md",
+  "gsd-core/workflows/plan-milestone-gaps.md",
+  "gsd-core/workflows/plan-phase.md",
+  "gsd-core/workflows/plan-phase/steps/closed-phase-gate.md",
+  "gsd-core/workflows/plan-phase/steps/prd-express-path.md",
+  "gsd-core/workflows/plan-phase/steps/windows-troubleshooting.md",
+  "gsd-core/workflows/plan-review-convergence.md",
+  "gsd-core/workflows/plant-seed.md",
+  "gsd-core/workflows/pr-branch.md",
+  "gsd-core/workflows/profile-user.md",
+  "gsd-core/workflows/progress.md",
+  "gsd-core/workflows/quick.md",
+  "gsd-core/workflows/reapply-patches.md",
+  "gsd-core/workflows/remove-phase.md",
+  "gsd-core/workflows/remove-workspace.md",
+  "gsd-core/workflows/resume-project.md",
+  "gsd-core/workflows/review.md",
+  "gsd-core/workflows/scan.md",
+  "gsd-core/workflows/secure-phase.md",
+  "gsd-core/workflows/session-report.md",
+  "gsd-core/workflows/settings-advanced.md",
+  "gsd-core/workflows/settings-integrations.md",
+  "gsd-core/workflows/settings.md",
+  "gsd-core/workflows/ship.md",
+  "gsd-core/workflows/sketch-wrap-up.md",
+  "gsd-core/workflows/sketch.md",
+  "gsd-core/workflows/smart-entry.md",
+  "gsd-core/workflows/spec-phase.md",
+  "gsd-core/workflows/spike-wrap-up.md",
+  "gsd-core/workflows/spike.md",
+  "gsd-core/workflows/stats.md",
+  "gsd-core/workflows/sync-skills.md",
+  "gsd-core/workflows/thread.md",
+  "gsd-core/workflows/transition.md",
+  "gsd-core/workflows/ui-phase.md",
+  "gsd-core/workflows/ui-review.md",
+  "gsd-core/workflows/ultraplan-phase.md",
+  "gsd-core/workflows/undo.md",
+  "gsd-core/workflows/update.md",
+  "gsd-core/workflows/validate-phase.md",
+  "gsd-core/workflows/verify-phase.md",
+  "gsd-core/workflows/verify-work.md",
+  "hooks/gsd-cursor-post-tool.js",
+  "hooks/gsd-cursor-pre-tool.js",
+  "hooks/gsd-cursor-session-start.js",
+  "hooks/gsd-cursor-stop.js",
+  "hooks/gsd-cursor-subagent-start.js",
+  "hooks/gsd-cursor-subagent-stop.js",
+  "scripts/changeset/README.md",
+  "scripts/changeset/cli.cjs",
+  "scripts/changeset/github-release-notes.cjs",
+  "scripts/changeset/lint.cjs",
+  "scripts/changeset/new.cjs",
+  "scripts/changeset/parse.cjs",
+  "scripts/changeset/render.cjs",
+  "scripts/changeset/serialize.cjs",
+  "scripts/fix-slash-commands.cjs",
+  "scripts/gen-capability-registry.cjs",
+  "scripts/gen-loop-host-contract.cjs",
+  "scripts/lib/allowlist-ratchet.cjs",
+  "scripts/lib/cli-exit.cjs",
+  "skills/gsd-add-tests/SKILL.md",
+  "skills/gsd-ai-integration-phase/SKILL.md",
+  "skills/gsd-audit-fix/SKILL.md",
+  "skills/gsd-audit-milestone/SKILL.md",
+  "skills/gsd-audit-uat/SKILL.md",
+  "skills/gsd-autonomous/SKILL.md",
+  "skills/gsd-capture/SKILL.md",
+  "skills/gsd-cleanup/SKILL.md",
+  "skills/gsd-code-review/SKILL.md",
+  "skills/gsd-complete-milestone/SKILL.md",
+  "skills/gsd-config/SKILL.md",
+  "skills/gsd-debug/SKILL.md",
+  "skills/gsd-discuss-phase/SKILL.md",
+  "skills/gsd-docs-update/SKILL.md",
+  "skills/gsd-eval-review/SKILL.md",
+  "skills/gsd-execute-phase/SKILL.md",
+  "skills/gsd-explore/SKILL.md",
+  "skills/gsd-extract-learnings/SKILL.md",
+  "skills/gsd-fast/SKILL.md",
+  "skills/gsd-forensics/SKILL.md",
+  "skills/gsd-graphify/SKILL.md",
+  "skills/gsd-health/SKILL.md",
+  "skills/gsd-help/SKILL.md",
+  "skills/gsd-import/SKILL.md",
+  "skills/gsd-inbox/SKILL.md",
+  "skills/gsd-ingest-docs/SKILL.md",
+  "skills/gsd-manager/SKILL.md",
+  "skills/gsd-map-codebase/SKILL.md",
+  "skills/gsd-mempalace-capture/SKILL.md",
+  "skills/gsd-mempalace-recall/SKILL.md",
+  "skills/gsd-milestone-summary/SKILL.md",
+  "skills/gsd-mvp-phase/SKILL.md",
+  "skills/gsd-new-milestone/SKILL.md",
+  "skills/gsd-new-project/SKILL.md",
+  "skills/gsd-next/SKILL.md",
+  "skills/gsd-ns-context/SKILL.md",
+  "skills/gsd-ns-ideate/SKILL.md",
+  "skills/gsd-ns-manage/SKILL.md",
+  "skills/gsd-ns-project/SKILL.md",
+  "skills/gsd-ns-review/SKILL.md",
+  "skills/gsd-ns-workflow/SKILL.md",
+  "skills/gsd-onboard/SKILL.md",
+  "skills/gsd-pause-work/SKILL.md",
+  "skills/gsd-phase/SKILL.md",
+  "skills/gsd-plan-phase/SKILL.md",
+  "skills/gsd-plan-review-convergence/SKILL.md",
+  "skills/gsd-pr-branch/SKILL.md",
+  "skills/gsd-profile-user/SKILL.md",
+  "skills/gsd-progress/SKILL.md",
+  "skills/gsd-quick/SKILL.md",
+  "skills/gsd-resume-work/SKILL.md",
+  "skills/gsd-review-backlog/SKILL.md",
+  "skills/gsd-review/SKILL.md",
+  "skills/gsd-secure-phase/SKILL.md",
+  "skills/gsd-settings/SKILL.md",
+  "skills/gsd-ship/SKILL.md",
+  "skills/gsd-sketch/SKILL.md",
+  "skills/gsd-spec-phase/SKILL.md",
+  "skills/gsd-spike/SKILL.md",
+  "skills/gsd-stats/SKILL.md",
+  "skills/gsd-surface/SKILL.md",
+  "skills/gsd-thread/SKILL.md",
+  "skills/gsd-ui-phase/SKILL.md",
+  "skills/gsd-ui-review/SKILL.md",
+  "skills/gsd-ultraplan-phase/SKILL.md",
+  "skills/gsd-undo/SKILL.md",
+  "skills/gsd-update/SKILL.md",
+  "skills/gsd-validate-phase/SKILL.md",
+  "skills/gsd-verify-work/SKILL.md",
+  "skills/gsd-workspace/SKILL.md",
+  "skills/gsd-workstreams/SKILL.md"
+]
diff --git a/tests/fixtures/install-tree/hermes.json b/tests/fixtures/install-tree/hermes.json
new file mode 100644
index 000000000..cb82f8eb8
--- /dev/null
+++ b/tests/fixtures/install-tree/hermes.json
@@ -0,0 +1,428 @@
+[
+  ".gsd-profile",
+  ".gsd/defaults.json",
+  "agents/gsd-advisor-researcher.md",
+  "agents/gsd-ai-researcher.md",
+  "agents/gsd-assumptions-analyzer.md",
+  "agents/gsd-code-fixer.md",
+  "agents/gsd-code-reviewer.md",
+  "agents/gsd-codebase-mapper.md",
+  "agents/gsd-debug-session-manager.md",
+  "agents/gsd-debugger.md",
+  "agents/gsd-doc-classifier.md",
+  "agents/gsd-doc-synthesizer.md",
+  "agents/gsd-doc-verifier.md",
+  "agents/gsd-doc-writer.md",
+  "agents/gsd-domain-researcher.md",
+  "agents/gsd-eval-auditor.md",
+  "agents/gsd-eval-planner.md",
+  "agents/gsd-executor.md",
+  "agents/gsd-framework-selector.md",
+  "agents/gsd-integration-checker.md",
+  "agents/gsd-intel-updater.md",
+  "agents/gsd-mempalace-curator.md",
+  "agents/gsd-nyquist-auditor.md",
+  "agents/gsd-pattern-mapper.md",
+  "agents/gsd-phase-researcher.md",
+  "agents/gsd-plan-checker.md",
+  "agents/gsd-planner.md",
+  "agents/gsd-project-researcher.md",
+  "agents/gsd-research-synthesizer.md",
+  "agents/gsd-roadmapper.md",
+  "agents/gsd-security-auditor.md",
+  "agents/gsd-ui-auditor.md",
+  "agents/gsd-ui-checker.md",
+  "agents/gsd-ui-researcher.md",
+  "agents/gsd-user-profiler.md",
+  "agents/gsd-verifier.md",
+  "gsd-core/VERSION",
+  "gsd-core/bin/check-latest-version.cjs",
+  "gsd-core/bin/ensure-runtime-build.cjs",
+  "gsd-core/bin/gsd-tools.cjs",
+  "gsd-core/bin/gsd_run",
+  "gsd-core/bin/shared/config-defaults.manifest.json",
+  "gsd-core/bin/shared/config-schema.manifest.json",
+  "gsd-core/bin/shared/model-catalog.json",
+  "gsd-core/bin/shared/runtime-aliases.manifest.json",
+  "gsd-core/bin/verify-reapply-patches.cjs",
+  "gsd-core/contexts/dev.md",
+  "gsd-core/contexts/research.md",
+  "gsd-core/contexts/review.md",
+  "gsd-core/references/agent-contracts.md",
+  "gsd-core/references/agent-skills-bootstrap.md",
+  "gsd-core/references/ai-evals.md",
+  "gsd-core/references/ai-frameworks.md",
+  "gsd-core/references/api-coverage.md",
+  "gsd-core/references/artifact-types.md",
+  "gsd-core/references/autonomous-smart-discuss.md",
+  "gsd-core/references/checkpoints.md",
+  "gsd-core/references/common-bug-patterns.md",
+  "gsd-core/references/context-budget.md",
+  "gsd-core/references/continuation-format.md",
+  "gsd-core/references/debugger-philosophy.md",
+  "gsd-core/references/decimal-phase-calculation.md",
+  "gsd-core/references/doc-conflict-engine.md",
+  "gsd-core/references/domain-probes.md",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/resolutions.json",
+  "gsd-core/references/edge-probe.md",
+  "gsd-core/references/execute-mvp-tdd.md",
+  "gsd-core/references/execute-phase-between-wave-reset.md",
+  "gsd-core/references/execute-phase-context-guard.md",
+  "gsd-core/references/execute-phase-wave-guard.md",
+  "gsd-core/references/executor-examples.md",
+  "gsd-core/references/few-shot-examples/plan-checker.md",
+  "gsd-core/references/few-shot-examples/verifier.md",
+  "gsd-core/references/gate-prompts.md",
+  "gsd-core/references/gates.md",
+  "gsd-core/references/git-integration.md",
+  "gsd-core/references/git-planning-commit.md",
+  "gsd-core/references/gsd-run-resolver.md",
+  "gsd-core/references/honest-verifier.md",
+  "gsd-core/references/ios-scaffold.md",
+  "gsd-core/references/loop-hook-dispatch.md",
+  "gsd-core/references/mandatory-initial-read.md",
+  "gsd-core/references/model-profile-resolution.md",
+  "gsd-core/references/model-profiles.md",
+  "gsd-core/references/mvp-concepts.md",
+  "gsd-core/references/phase-argument-parsing.md",
+  "gsd-core/references/planner-antipatterns.md",
+  "gsd-core/references/planner-chunked.md",
+  "gsd-core/references/planner-gap-closure.md",
+  "gsd-core/references/planner-graphify-auto-update.md",
+  "gsd-core/references/planner-guidance.md",
+  "gsd-core/references/planner-human-verify-mode.md",
+  "gsd-core/references/planner-interface-context.md",
+  "gsd-core/references/planner-load-graph-context.md",
+  "gsd-core/references/planner-mvp-mode.md",
+  "gsd-core/references/planner-reviews.md",
+  "gsd-core/references/planner-revision.md",
+  "gsd-core/references/planner-source-audit.md",
+  "gsd-core/references/planning-config.md",
+  "gsd-core/references/prohibition-probe-fixtures/01-streak-reminder/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/02-clean-utility/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/03-multi-prohibition/expected.json",
+  "gsd-core/references/prohibition-probe.md",
+  "gsd-core/references/project-skills-discovery.md",
+  "gsd-core/references/questioning.md",
+  "gsd-core/references/research-documentation-lookup.md",
+  "gsd-core/references/research-philosophy.md",
+  "gsd-core/references/research-verification-protocol.md",
+  "gsd-core/references/reviewer-instances.md",
+  "gsd-core/references/revision-loop.md",
+  "gsd-core/references/scout-codebase.md",
+  "gsd-core/references/security-asvs-levels.md",
+  "gsd-core/references/skeleton-template.md",
+  "gsd-core/references/sketch-interactivity.md",
+  "gsd-core/references/sketch-theme-system.md",
+  "gsd-core/references/sketch-tooling.md",
+  "gsd-core/references/sketch-variant-patterns.md",
+  "gsd-core/references/specless-probe-fallback.md",
+  "gsd-core/references/spidr-splitting.md",
+  "gsd-core/references/tdd.md",
+  "gsd-core/references/thinking-models-debug.md",
+  "gsd-core/references/thinking-models-execution.md",
+  "gsd-core/references/thinking-models-planning.md",
+  "gsd-core/references/thinking-models-research.md",
+  "gsd-core/references/thinking-models-verification.md",
+  "gsd-core/references/thinking-partner.md",
+  "gsd-core/references/ui-brand.md",
+  "gsd-core/references/ui-consideration-probe.md",
+  "gsd-core/references/universal-anti-patterns.md",
+  "gsd-core/references/untrusted-input-boundary.md",
+  "gsd-core/references/user-profiling.md",
+  "gsd-core/references/user-story-template.md",
+  "gsd-core/references/verification-overrides.md",
+  "gsd-core/references/verification-patterns.md",
+  "gsd-core/references/verify-mvp-mode.md",
+  "gsd-core/references/workstream-flag.md",
+  "gsd-core/references/worktree-branch-check.md",
+  "gsd-core/references/worktree-path-safety.md",
+  "gsd-core/templates/AI-SPEC.md",
+  "gsd-core/templates/DEBUG.md",
+  "gsd-core/templates/README.md",
+  "gsd-core/templates/SECURITY.md",
+  "gsd-core/templates/UAT.md",
+  "gsd-core/templates/UI-SPEC.md",
+  "gsd-core/templates/VALIDATION.md",
+  "gsd-core/templates/claude-md.md",
+  "gsd-core/templates/codebase/architecture.md",
+  "gsd-core/templates/codebase/concerns.md",
+  "gsd-core/templates/codebase/conventions.md",
+  "gsd-core/templates/codebase/integrations.md",
+  "gsd-core/templates/codebase/stack.md",
+  "gsd-core/templates/codebase/structure.md",
+  "gsd-core/templates/codebase/testing.md",
+  "gsd-core/templates/config.json",
+  "gsd-core/templates/context.md",
+  "gsd-core/templates/continue-here.md",
+  "gsd-core/templates/copilot-instructions.md",
+  "gsd-core/templates/debug-subagent-prompt.md",
+  "gsd-core/templates/dev-preferences.md",
+  "gsd-core/templates/discovery.md",
+  "gsd-core/templates/discussion-log.md",
+  "gsd-core/templates/milestone-archive.md",
+  "gsd-core/templates/milestone.md",
+  "gsd-core/templates/phase-prompt.md",
+  "gsd-core/templates/planner-subagent-prompt.md",
+  "gsd-core/templates/project.md",
+  "gsd-core/templates/requirements.md",
+  "gsd-core/templates/research-project/ARCHITECTURE.md",
+  "gsd-core/templates/research-project/FEATURES.md",
+  "gsd-core/templates/research-project/PITFALLS.md",
+  "gsd-core/templates/research-project/STACK.md",
+  "gsd-core/templates/research-project/SUMMARY.md",
+  "gsd-core/templates/research.md",
+  "gsd-core/templates/retrospective.md",
+  "gsd-core/templates/roadmap.md",
+  "gsd-core/templates/spec.md",
+  "gsd-core/templates/state.md",
+  "gsd-core/templates/summary-complex.md",
+  "gsd-core/templates/summary-minimal.md",
+  "gsd-core/templates/summary-standard.md",
+  "gsd-core/templates/summary.md",
+  "gsd-core/templates/user-profile.md",
+  "gsd-core/templates/user-setup.md",
+  "gsd-core/templates/verification-report.md",
+  "gsd-core/workflows/_runtime-launcher.snippet.sh",
+  "gsd-core/workflows/add-backlog.md",
+  "gsd-core/workflows/add-phase.md",
+  "gsd-core/workflows/add-tests.md",
+  "gsd-core/workflows/add-todo.md",
+  "gsd-core/workflows/ai-integration-phase.md",
+  "gsd-core/workflows/analyze-dependencies.md",
+  "gsd-core/workflows/audit-fix.md",
+  "gsd-core/workflows/audit-milestone.md",
+  "gsd-core/workflows/audit-uat.md",
+  "gsd-core/workflows/autonomous.md",
+  "gsd-core/workflows/check-todos.md",
+  "gsd-core/workflows/cleanup.md",
+  "gsd-core/workflows/code-review-fix.md",
+  "gsd-core/workflows/code-review.md",
+  "gsd-core/workflows/complete-milestone.md",
+  "gsd-core/workflows/debug.md",
+  "gsd-core/workflows/diagnose-issues.md",
+  "gsd-core/workflows/discovery-phase.md",
+  "gsd-core/workflows/discuss-phase-assumptions.md",
+  "gsd-core/workflows/discuss-phase-power.md",
+  "gsd-core/workflows/discuss-phase.md",
+  "gsd-core/workflows/discuss-phase/modes/advisor.md",
+  "gsd-core/workflows/discuss-phase/modes/all.md",
+  "gsd-core/workflows/discuss-phase/modes/analyze.md",
+  "gsd-core/workflows/discuss-phase/modes/auto.md",
+  "gsd-core/workflows/discuss-phase/modes/batch.md",
+  "gsd-core/workflows/discuss-phase/modes/chain.md",
+  "gsd-core/workflows/discuss-phase/modes/default.md",
+  "gsd-core/workflows/discuss-phase/modes/power.md",
+  "gsd-core/workflows/discuss-phase/modes/text.md",
+  "gsd-core/workflows/discuss-phase/templates/checkpoint.json",
+  "gsd-core/workflows/discuss-phase/templates/context.md",
+  "gsd-core/workflows/discuss-phase/templates/discussion-log.md",
+  "gsd-core/workflows/do.md",
+  "gsd-core/workflows/docs-update.md",
+  "gsd-core/workflows/edit-phase.md",
+  "gsd-core/workflows/eval-review.md",
+  "gsd-core/workflows/execute-phase.md",
+  "gsd-core/workflows/execute-phase/steps/codebase-drift-gate.md",
+  "gsd-core/workflows/execute-phase/steps/per-plan-worktree-gate.md",
+  "gsd-core/workflows/execute-phase/steps/post-merge-gate.md",
+  "gsd-core/workflows/execute-phase/steps/regression-gate.md",
+  "gsd-core/workflows/execute-phase/steps/worktree-recovery-policy.md",
+  "gsd-core/workflows/execute-plan.md",
+  "gsd-core/workflows/explore.md",
+  "gsd-core/workflows/extract-learnings.md",
+  "gsd-core/workflows/fast.md",
+  "gsd-core/workflows/forensics.md",
+  "gsd-core/workflows/graduation.md",
+  "gsd-core/workflows/health.md",
+  "gsd-core/workflows/help.md",
+  "gsd-core/workflows/help/modes/brief.md",
+  "gsd-core/workflows/help/modes/default.md",
+  "gsd-core/workflows/help/modes/full.md",
+  "gsd-core/workflows/help/modes/topic.md",
+  "gsd-core/workflows/import.md",
+  "gsd-core/workflows/inbox.md",
+  "gsd-core/workflows/ingest-docs.md",
+  "gsd-core/workflows/insert-phase.md",
+  "gsd-core/workflows/list-phase-assumptions.md",
+  "gsd-core/workflows/list-seeds.md",
+  "gsd-core/workflows/list-workspaces.md",
+  "gsd-core/workflows/manager.md",
+  "gsd-core/workflows/map-codebase.md",
+  "gsd-core/workflows/milestone-summary.md",
+  "gsd-core/workflows/mvp-phase.md",
+  "gsd-core/workflows/new-milestone.md",
+  "gsd-core/workflows/new-project.md",
+  "gsd-core/workflows/new-workspace.md",
+  "gsd-core/workflows/next.md",
+  "gsd-core/workflows/node-repair.md",
+  "gsd-core/workflows/note.md",
+  "gsd-core/workflows/onboard.md",
+  "gsd-core/workflows/pause-work.md",
+  "gsd-core/workflows/plan-milestone-gaps.md",
+  "gsd-core/workflows/plan-phase.md",
+  "gsd-core/workflows/plan-phase/steps/closed-phase-gate.md",
+  "gsd-core/workflows/plan-phase/steps/prd-express-path.md",
+  "gsd-core/workflows/plan-phase/steps/windows-troubleshooting.md",
+  "gsd-core/workflows/plan-review-convergence.md",
+  "gsd-core/workflows/plant-seed.md",
+  "gsd-core/workflows/pr-branch.md",
+  "gsd-core/workflows/profile-user.md",
+  "gsd-core/workflows/progress.md",
+  "gsd-core/workflows/quick.md",
+  "gsd-core/workflows/reapply-patches.md",
+  "gsd-core/workflows/remove-phase.md",
+  "gsd-core/workflows/remove-workspace.md",
+  "gsd-core/workflows/resume-project.md",
+  "gsd-core/workflows/review.md",
+  "gsd-core/workflows/scan.md",
+  "gsd-core/workflows/secure-phase.md",
+  "gsd-core/workflows/session-report.md",
+  "gsd-core/workflows/settings-advanced.md",
+  "gsd-core/workflows/settings-integrations.md",
+  "gsd-core/workflows/settings.md",
+  "gsd-core/workflows/ship.md",
+  "gsd-core/workflows/sketch-wrap-up.md",
+  "gsd-core/workflows/sketch.md",
+  "gsd-core/workflows/smart-entry.md",
+  "gsd-core/workflows/spec-phase.md",
+  "gsd-core/workflows/spike-wrap-up.md",
+  "gsd-core/workflows/spike.md",
+  "gsd-core/workflows/stats.md",
+  "gsd-core/workflows/sync-skills.md",
+  "gsd-core/workflows/thread.md",
+  "gsd-core/workflows/transition.md",
+  "gsd-core/workflows/ui-phase.md",
+  "gsd-core/workflows/ui-review.md",
+  "gsd-core/workflows/ultraplan-phase.md",
+  "gsd-core/workflows/undo.md",
+  "gsd-core/workflows/update.md",
+  "gsd-core/workflows/validate-phase.md",
+  "gsd-core/workflows/verify-phase.md",
+  "gsd-core/workflows/verify-work.md",
+  "hooks/gsd-check-update-worker.js",
+  "hooks/gsd-check-update.js",
+  "hooks/gsd-config-reload.js",
+  "hooks/gsd-context-monitor.js",
+  "hooks/gsd-cursor-post-tool.js",
+  "hooks/gsd-cursor-pre-tool.js",
+  "hooks/gsd-cursor-session-start.js",
+  "hooks/gsd-cursor-stop.js",
+  "hooks/gsd-cursor-subagent-start.js",
+  "hooks/gsd-cursor-subagent-stop.js",
+  "hooks/gsd-ensure-canonical-path.js",
+  "hooks/gsd-graphify-update.sh",
+  "hooks/gsd-phase-boundary.sh",
+  "hooks/gsd-prompt-guard.js",
+  "hooks/gsd-read-guard.js",
+  "hooks/gsd-read-injection-scanner.js",
+  "hooks/gsd-session-state.sh",
+  "hooks/gsd-statusline.js",
+  "hooks/gsd-update-banner.js",
+  "hooks/gsd-validate-commit.sh",
+  "hooks/gsd-windsurf-pre-command.js",
+  "hooks/gsd-windsurf-pre-write.js",
+  "hooks/gsd-workflow-guard.js",
+  "hooks/gsd-worktree-path-guard.js",
+  "hooks/lib/git-cmd.js",
+  "hooks/lib/gsd-graphify-rebuild.sh",
+  "hooks/managed-hooks-registry.cjs",
+  "package.json",
+  "scripts/changeset/README.md",
+  "scripts/changeset/cli.cjs",
+  "scripts/changeset/github-release-notes.cjs",
+  "scripts/changeset/lint.cjs",
+  "scripts/changeset/new.cjs",
+  "scripts/changeset/parse.cjs",
+  "scripts/changeset/render.cjs",
+  "scripts/changeset/serialize.cjs",
+  "scripts/fix-slash-commands.cjs",
+  "scripts/gen-capability-registry.cjs",
+  "scripts/gen-loop-host-contract.cjs",
+  "scripts/lib/allowlist-ratchet.cjs",
+  "scripts/lib/cli-exit.cjs",
+  "skills/gsd/DESCRIPTION.md",
+  "skills/gsd/gsd-ns-context/SKILL.md",
+  "skills/gsd/gsd-ns-context/skills/docs-update/SKILL.md",
+  "skills/gsd/gsd-ns-context/skills/extract-learnings/SKILL.md",
+  "skills/gsd/gsd-ns-context/skills/graphify/SKILL.md",
+  "skills/gsd/gsd-ns-context/skills/map-codebase/SKILL.md",
+  "skills/gsd/gsd-ns-context/skills/mempalace-capture/SKILL.md",
+  "skills/gsd/gsd-ns-context/skills/mempalace-recall/SKILL.md",
+  "skills/gsd/gsd-ns-ideate/SKILL.md",
+  "skills/gsd/gsd-ns-ideate/skills/capture/SKILL.md",
+  "skills/gsd/gsd-ns-ideate/skills/explore/SKILL.md",
+  "skills/gsd/gsd-ns-ideate/skills/sketch/SKILL.md",
+  "skills/gsd/gsd-ns-ideate/skills/spec-phase/SKILL.md",
+  "skills/gsd/gsd-ns-ideate/skills/spike/SKILL.md",
+  "skills/gsd/gsd-ns-manage/SKILL.md",
+  "skills/gsd/gsd-ns-manage/skills/cleanup/SKILL.md",
+  "skills/gsd/gsd-ns-manage/skills/config/SKILL.md",
+  "skills/gsd/gsd-ns-manage/skills/health/SKILL.md",
+  "skills/gsd/gsd-ns-manage/skills/help/SKILL.md",
+  "skills/gsd/gsd-ns-manage/skills/inbox/SKILL.md",
+  "skills/gsd/gsd-ns-manage/skills/manager/SKILL.md",
+  "skills/gsd/gsd-ns-manage/skills/pause-work/SKILL.md",
+  "skills/gsd/gsd-ns-manage/skills/pr-branch/SKILL.md",
+  "skills/gsd/gsd-ns-manage/skills/resume-work/SKILL.md",
+  "skills/gsd/gsd-ns-manage/skills/settings/SKILL.md",
+  "skills/gsd/gsd-ns-manage/skills/ship/SKILL.md",
+  "skills/gsd/gsd-ns-manage/skills/stats/SKILL.md",
+  "skills/gsd/gsd-ns-manage/skills/surface/SKILL.md",
+  "skills/gsd/gsd-ns-manage/skills/thread/SKILL.md",
+  "skills/gsd/gsd-ns-manage/skills/undo/SKILL.md",
+  "skills/gsd/gsd-ns-manage/skills/update/SKILL.md",
+  "skills/gsd/gsd-ns-manage/skills/workspace/SKILL.md",
+  "skills/gsd/gsd-ns-manage/skills/workstreams/SKILL.md",
+  "skills/gsd/gsd-ns-project/SKILL.md",
+  "skills/gsd/gsd-ns-project/skills/audit-milestone/SKILL.md",
+  "skills/gsd/gsd-ns-project/skills/complete-milestone/SKILL.md",
+  "skills/gsd/gsd-ns-project/skills/import/SKILL.md",
+  "skills/gsd/gsd-ns-project/skills/ingest-docs/SKILL.md",
+  "skills/gsd/gsd-ns-project/skills/milestone-summary/SKILL.md",
+  "skills/gsd/gsd-ns-project/skills/new-milestone/SKILL.md",
+  "skills/gsd/gsd-ns-project/skills/new-project/SKILL.md",
+  "skills/gsd/gsd-ns-project/skills/onboard/SKILL.md",
+  "skills/gsd/gsd-ns-project/skills/profile-user/SKILL.md",
+  "skills/gsd/gsd-ns-project/skills/review-backlog/SKILL.md",
+  "skills/gsd/gsd-ns-review/SKILL.md",
+  "skills/gsd/gsd-ns-review/skills/audit-fix/SKILL.md",
+  "skills/gsd/gsd-ns-review/skills/audit-uat/SKILL.md",
+  "skills/gsd/gsd-ns-review/skills/code-review/SKILL.md",
+  "skills/gsd/gsd-ns-review/skills/debug/SKILL.md",
+  "skills/gsd/gsd-ns-review/skills/eval-review/SKILL.md",
+  "skills/gsd/gsd-ns-review/skills/forensics/SKILL.md",
+  "skills/gsd/gsd-ns-review/skills/review/SKILL.md",
+  "skills/gsd/gsd-ns-review/skills/secure-phase/SKILL.md",
+  "skills/gsd/gsd-ns-review/skills/ui-phase/SKILL.md",
+  "skills/gsd/gsd-ns-review/skills/ui-review/SKILL.md",
+  "skills/gsd/gsd-ns-review/skills/validate-phase/SKILL.md",
+  "skills/gsd/gsd-ns-workflow/SKILL.md",
+  "skills/gsd/gsd-ns-workflow/skills/add-tests/SKILL.md",
+  "skills/gsd/gsd-ns-workflow/skills/ai-integration-phase/SKILL.md",
+  "skills/gsd/gsd-ns-workflow/skills/autonomous/SKILL.md",
+  "skills/gsd/gsd-ns-workflow/skills/discuss-phase/SKILL.md",
+  "skills/gsd/gsd-ns-workflow/skills/execute-phase/SKILL.md",
+  "skills/gsd/gsd-ns-workflow/skills/fast/SKILL.md",
+  "skills/gsd/gsd-ns-workflow/skills/mvp-phase/SKILL.md",
+  "skills/gsd/gsd-ns-workflow/skills/next/SKILL.md",
+  "skills/gsd/gsd-ns-workflow/skills/phase/SKILL.md",
+  "skills/gsd/gsd-ns-workflow/skills/plan-phase/SKILL.md",
+  "skills/gsd/gsd-ns-workflow/skills/plan-review-convergence/SKILL.md",
+  "skills/gsd/gsd-ns-workflow/skills/progress/SKILL.md",
+  "skills/gsd/gsd-ns-workflow/skills/quick/SKILL.md",
+  "skills/gsd/gsd-ns-workflow/skills/spec-phase/SKILL.md",
+  "skills/gsd/gsd-ns-workflow/skills/ultraplan-phase/SKILL.md",
+  "skills/gsd/gsd-ns-workflow/skills/verify-work/SKILL.md"
+]
diff --git a/tests/fixtures/install-tree/kilo.json b/tests/fixtures/install-tree/kilo.json
new file mode 100644
index 000000000..93ff07f73
--- /dev/null
+++ b/tests/fixtures/install-tree/kilo.json
@@ -0,0 +1,471 @@
+[
+  ".gsd-profile",
+  ".gsd/defaults.json",
+  "agents/gsd-advisor-researcher.md",
+  "agents/gsd-ai-researcher.md",
+  "agents/gsd-assumptions-analyzer.md",
+  "agents/gsd-code-fixer.md",
+  "agents/gsd-code-reviewer.md",
+  "agents/gsd-codebase-mapper.md",
+  "agents/gsd-debug-session-manager.md",
+  "agents/gsd-debugger.md",
+  "agents/gsd-doc-classifier.md",
+  "agents/gsd-doc-synthesizer.md",
+  "agents/gsd-doc-verifier.md",
+  "agents/gsd-doc-writer.md",
+  "agents/gsd-domain-researcher.md",
+  "agents/gsd-eval-auditor.md",
+  "agents/gsd-eval-planner.md",
+  "agents/gsd-executor.md",
+  "agents/gsd-framework-selector.md",
+  "agents/gsd-integration-checker.md",
+  "agents/gsd-intel-updater.md",
+  "agents/gsd-mempalace-curator.md",
+  "agents/gsd-nyquist-auditor.md",
+  "agents/gsd-pattern-mapper.md",
+  "agents/gsd-phase-researcher.md",
+  "agents/gsd-plan-checker.md",
+  "agents/gsd-planner.md",
+  "agents/gsd-project-researcher.md",
+  "agents/gsd-research-synthesizer.md",
+  "agents/gsd-roadmapper.md",
+  "agents/gsd-security-auditor.md",
+  "agents/gsd-ui-auditor.md",
+  "agents/gsd-ui-checker.md",
+  "agents/gsd-ui-researcher.md",
+  "agents/gsd-user-profiler.md",
+  "agents/gsd-verifier.md",
+  "command/gsd-add-tests.md",
+  "command/gsd-ai-integration-phase.md",
+  "command/gsd-audit-fix.md",
+  "command/gsd-audit-milestone.md",
+  "command/gsd-audit-uat.md",
+  "command/gsd-autonomous.md",
+  "command/gsd-capture.md",
+  "command/gsd-cleanup.md",
+  "command/gsd-code-review.md",
+  "command/gsd-complete-milestone.md",
+  "command/gsd-config.md",
+  "command/gsd-debug.md",
+  "command/gsd-discuss-phase.md",
+  "command/gsd-docs-update.md",
+  "command/gsd-eval-review.md",
+  "command/gsd-execute-phase.md",
+  "command/gsd-explore.md",
+  "command/gsd-extract-learnings.md",
+  "command/gsd-fast.md",
+  "command/gsd-forensics.md",
+  "command/gsd-graphify.md",
+  "command/gsd-health.md",
+  "command/gsd-help.md",
+  "command/gsd-import.md",
+  "command/gsd-inbox.md",
+  "command/gsd-ingest-docs.md",
+  "command/gsd-manager.md",
+  "command/gsd-map-codebase.md",
+  "command/gsd-mempalace-capture.md",
+  "command/gsd-mempalace-recall.md",
+  "command/gsd-milestone-summary.md",
+  "command/gsd-mvp-phase.md",
+  "command/gsd-new-milestone.md",
+  "command/gsd-new-project.md",
+  "command/gsd-next.md",
+  "command/gsd-ns-context.md",
+  "command/gsd-ns-ideate.md",
+  "command/gsd-ns-manage.md",
+  "command/gsd-ns-project.md",
+  "command/gsd-ns-review.md",
+  "command/gsd-ns-workflow.md",
+  "command/gsd-onboard.md",
+  "command/gsd-pause-work.md",
+  "command/gsd-phase.md",
+  "command/gsd-plan-phase.md",
+  "command/gsd-plan-review-convergence.md",
+  "command/gsd-pr-branch.md",
+  "command/gsd-profile-user.md",
+  "command/gsd-progress.md",
+  "command/gsd-quick.md",
+  "command/gsd-resume-work.md",
+  "command/gsd-review-backlog.md",
+  "command/gsd-review.md",
+  "command/gsd-secure-phase.md",
+  "command/gsd-settings.md",
+  "command/gsd-ship.md",
+  "command/gsd-sketch.md",
+  "command/gsd-spec-phase.md",
+  "command/gsd-spike.md",
+  "command/gsd-stats.md",
+  "command/gsd-surface.md",
+  "command/gsd-thread.md",
+  "command/gsd-ui-phase.md",
+  "command/gsd-ui-review.md",
+  "command/gsd-ultraplan-phase.md",
+  "command/gsd-undo.md",
+  "command/gsd-update.md",
+  "command/gsd-validate-phase.md",
+  "command/gsd-verify-work.md",
+  "command/gsd-workspace.md",
+  "command/gsd-workstreams.md",
+  "gsd-core/VERSION",
+  "gsd-core/bin/check-latest-version.cjs",
+  "gsd-core/bin/ensure-runtime-build.cjs",
+  "gsd-core/bin/gsd-tools.cjs",
+  "gsd-core/bin/gsd_run",
+  "gsd-core/bin/shared/config-defaults.manifest.json",
+  "gsd-core/bin/shared/config-schema.manifest.json",
+  "gsd-core/bin/shared/model-catalog.json",
+  "gsd-core/bin/shared/runtime-aliases.manifest.json",
+  "gsd-core/bin/verify-reapply-patches.cjs",
+  "gsd-core/contexts/dev.md",
+  "gsd-core/contexts/research.md",
+  "gsd-core/contexts/review.md",
+  "gsd-core/references/agent-contracts.md",
+  "gsd-core/references/agent-skills-bootstrap.md",
+  "gsd-core/references/ai-evals.md",
+  "gsd-core/references/ai-frameworks.md",
+  "gsd-core/references/api-coverage.md",
+  "gsd-core/references/artifact-types.md",
+  "gsd-core/references/autonomous-smart-discuss.md",
+  "gsd-core/references/checkpoints.md",
+  "gsd-core/references/common-bug-patterns.md",
+  "gsd-core/references/context-budget.md",
+  "gsd-core/references/continuation-format.md",
+  "gsd-core/references/debugger-philosophy.md",
+  "gsd-core/references/decimal-phase-calculation.md",
+  "gsd-core/references/doc-conflict-engine.md",
+  "gsd-core/references/domain-probes.md",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/resolutions.json",
+  "gsd-core/references/edge-probe.md",
+  "gsd-core/references/execute-mvp-tdd.md",
+  "gsd-core/references/execute-phase-between-wave-reset.md",
+  "gsd-core/references/execute-phase-context-guard.md",
+  "gsd-core/references/execute-phase-wave-guard.md",
+  "gsd-core/references/executor-examples.md",
+  "gsd-core/references/few-shot-examples/plan-checker.md",
+  "gsd-core/references/few-shot-examples/verifier.md",
+  "gsd-core/references/gate-prompts.md",
+  "gsd-core/references/gates.md",
+  "gsd-core/references/git-integration.md",
+  "gsd-core/references/git-planning-commit.md",
+  "gsd-core/references/gsd-run-resolver.md",
+  "gsd-core/references/honest-verifier.md",
+  "gsd-core/references/ios-scaffold.md",
+  "gsd-core/references/loop-hook-dispatch.md",
+  "gsd-core/references/mandatory-initial-read.md",
+  "gsd-core/references/model-profile-resolution.md",
+  "gsd-core/references/model-profiles.md",
+  "gsd-core/references/mvp-concepts.md",
+  "gsd-core/references/phase-argument-parsing.md",
+  "gsd-core/references/planner-antipatterns.md",
+  "gsd-core/references/planner-chunked.md",
+  "gsd-core/references/planner-gap-closure.md",
+  "gsd-core/references/planner-graphify-auto-update.md",
+  "gsd-core/references/planner-guidance.md",
+  "gsd-core/references/planner-human-verify-mode.md",
+  "gsd-core/references/planner-interface-context.md",
+  "gsd-core/references/planner-load-graph-context.md",
+  "gsd-core/references/planner-mvp-mode.md",
+  "gsd-core/references/planner-reviews.md",
+  "gsd-core/references/planner-revision.md",
+  "gsd-core/references/planner-source-audit.md",
+  "gsd-core/references/planning-config.md",
+  "gsd-core/references/prohibition-probe-fixtures/01-streak-reminder/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/02-clean-utility/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/03-multi-prohibition/expected.json",
+  "gsd-core/references/prohibition-probe.md",
+  "gsd-core/references/project-skills-discovery.md",
+  "gsd-core/references/questioning.md",
+  "gsd-core/references/research-documentation-lookup.md",
+  "gsd-core/references/research-philosophy.md",
+  "gsd-core/references/research-verification-protocol.md",
+  "gsd-core/references/reviewer-instances.md",
+  "gsd-core/references/revision-loop.md",
+  "gsd-core/references/scout-codebase.md",
+  "gsd-core/references/security-asvs-levels.md",
+  "gsd-core/references/skeleton-template.md",
+  "gsd-core/references/sketch-interactivity.md",
+  "gsd-core/references/sketch-theme-system.md",
+  "gsd-core/references/sketch-tooling.md",
+  "gsd-core/references/sketch-variant-patterns.md",
+  "gsd-core/references/specless-probe-fallback.md",
+  "gsd-core/references/spidr-splitting.md",
+  "gsd-core/references/tdd.md",
+  "gsd-core/references/thinking-models-debug.md",
+  "gsd-core/references/thinking-models-execution.md",
+  "gsd-core/references/thinking-models-planning.md",
+  "gsd-core/references/thinking-models-research.md",
+  "gsd-core/references/thinking-models-verification.md",
+  "gsd-core/references/thinking-partner.md",
+  "gsd-core/references/ui-brand.md",
+  "gsd-core/references/ui-consideration-probe.md",
+  "gsd-core/references/universal-anti-patterns.md",
+  "gsd-core/references/untrusted-input-boundary.md",
+  "gsd-core/references/user-profiling.md",
+  "gsd-core/references/user-story-template.md",
+  "gsd-core/references/verification-overrides.md",
+  "gsd-core/references/verification-patterns.md",
+  "gsd-core/references/verify-mvp-mode.md",
+  "gsd-core/references/workstream-flag.md",
+  "gsd-core/references/worktree-branch-check.md",
+  "gsd-core/references/worktree-path-safety.md",
+  "gsd-core/templates/AI-SPEC.md",
+  "gsd-core/templates/DEBUG.md",
+  "gsd-core/templates/README.md",
+  "gsd-core/templates/SECURITY.md",
+  "gsd-core/templates/UAT.md",
+  "gsd-core/templates/UI-SPEC.md",
+  "gsd-core/templates/VALIDATION.md",
+  "gsd-core/templates/claude-md.md",
+  "gsd-core/templates/codebase/architecture.md",
+  "gsd-core/templates/codebase/concerns.md",
+  "gsd-core/templates/codebase/conventions.md",
+  "gsd-core/templates/codebase/integrations.md",
+  "gsd-core/templates/codebase/stack.md",
+  "gsd-core/templates/codebase/structure.md",
+  "gsd-core/templates/codebase/testing.md",
+  "gsd-core/templates/config.json",
+  "gsd-core/templates/context.md",
+  "gsd-core/templates/continue-here.md",
+  "gsd-core/templates/copilot-instructions.md",
+  "gsd-core/templates/debug-subagent-prompt.md",
+  "gsd-core/templates/dev-preferences.md",
+  "gsd-core/templates/discovery.md",
+  "gsd-core/templates/discussion-log.md",
+  "gsd-core/templates/milestone-archive.md",
+  "gsd-core/templates/milestone.md",
+  "gsd-core/templates/phase-prompt.md",
+  "gsd-core/templates/planner-subagent-prompt.md",
+  "gsd-core/templates/project.md",
+  "gsd-core/templates/requirements.md",
+  "gsd-core/templates/research-project/ARCHITECTURE.md",
+  "gsd-core/templates/research-project/FEATURES.md",
+  "gsd-core/templates/research-project/PITFALLS.md",
+  "gsd-core/templates/research-project/STACK.md",
+  "gsd-core/templates/research-project/SUMMARY.md",
+  "gsd-core/templates/research.md",
+  "gsd-core/templates/retrospective.md",
+  "gsd-core/templates/roadmap.md",
+  "gsd-core/templates/spec.md",
+  "gsd-core/templates/state.md",
+  "gsd-core/templates/summary-complex.md",
+  "gsd-core/templates/summary-minimal.md",
+  "gsd-core/templates/summary-standard.md",
+  "gsd-core/templates/summary.md",
+  "gsd-core/templates/user-profile.md",
+  "gsd-core/templates/user-setup.md",
+  "gsd-core/templates/verification-report.md",
+  "gsd-core/workflows/_runtime-launcher.snippet.sh",
+  "gsd-core/workflows/add-backlog.md",
+  "gsd-core/workflows/add-phase.md",
+  "gsd-core/workflows/add-tests.md",
+  "gsd-core/workflows/add-todo.md",
+  "gsd-core/workflows/ai-integration-phase.md",
+  "gsd-core/workflows/analyze-dependencies.md",
+  "gsd-core/workflows/audit-fix.md",
+  "gsd-core/workflows/audit-milestone.md",
+  "gsd-core/workflows/audit-uat.md",
+  "gsd-core/workflows/autonomous.md",
+  "gsd-core/workflows/check-todos.md",
+  "gsd-core/workflows/cleanup.md",
+  "gsd-core/workflows/code-review-fix.md",
+  "gsd-core/workflows/code-review.md",
+  "gsd-core/workflows/complete-milestone.md",
+  "gsd-core/workflows/debug.md",
+  "gsd-core/workflows/diagnose-issues.md",
+  "gsd-core/workflows/discovery-phase.md",
+  "gsd-core/workflows/discuss-phase-assumptions.md",
+  "gsd-core/workflows/discuss-phase-power.md",
+  "gsd-core/workflows/discuss-phase.md",
+  "gsd-core/workflows/discuss-phase/modes/advisor.md",
+  "gsd-core/workflows/discuss-phase/modes/all.md",
+  "gsd-core/workflows/discuss-phase/modes/analyze.md",
+  "gsd-core/workflows/discuss-phase/modes/auto.md",
+  "gsd-core/workflows/discuss-phase/modes/batch.md",
+  "gsd-core/workflows/discuss-phase/modes/chain.md",
+  "gsd-core/workflows/discuss-phase/modes/default.md",
+  "gsd-core/workflows/discuss-phase/modes/power.md",
+  "gsd-core/workflows/discuss-phase/modes/text.md",
+  "gsd-core/workflows/discuss-phase/templates/checkpoint.json",
+  "gsd-core/workflows/discuss-phase/templates/context.md",
+  "gsd-core/workflows/discuss-phase/templates/discussion-log.md",
+  "gsd-core/workflows/do.md",
+  "gsd-core/workflows/docs-update.md",
+  "gsd-core/workflows/edit-phase.md",
+  "gsd-core/workflows/eval-review.md",
+  "gsd-core/workflows/execute-phase.md",
+  "gsd-core/workflows/execute-phase/steps/codebase-drift-gate.md",
+  "gsd-core/workflows/execute-phase/steps/per-plan-worktree-gate.md",
+  "gsd-core/workflows/execute-phase/steps/post-merge-gate.md",
+  "gsd-core/workflows/execute-phase/steps/regression-gate.md",
+  "gsd-core/workflows/execute-phase/steps/worktree-recovery-policy.md",
+  "gsd-core/workflows/execute-plan.md",
+  "gsd-core/workflows/explore.md",
+  "gsd-core/workflows/extract-learnings.md",
+  "gsd-core/workflows/fast.md",
+  "gsd-core/workflows/forensics.md",
+  "gsd-core/workflows/graduation.md",
+  "gsd-core/workflows/health.md",
+  "gsd-core/workflows/help.md",
+  "gsd-core/workflows/help/modes/brief.md",
+  "gsd-core/workflows/help/modes/default.md",
+  "gsd-core/workflows/help/modes/full.md",
+  "gsd-core/workflows/help/modes/topic.md",
+  "gsd-core/workflows/import.md",
+  "gsd-core/workflows/inbox.md",
+  "gsd-core/workflows/ingest-docs.md",
+  "gsd-core/workflows/insert-phase.md",
+  "gsd-core/workflows/list-phase-assumptions.md",
+  "gsd-core/workflows/list-seeds.md",
+  "gsd-core/workflows/list-workspaces.md",
+  "gsd-core/workflows/manager.md",
+  "gsd-core/workflows/map-codebase.md",
+  "gsd-core/workflows/milestone-summary.md",
+  "gsd-core/workflows/mvp-phase.md",
+  "gsd-core/workflows/new-milestone.md",
+  "gsd-core/workflows/new-project.md",
+  "gsd-core/workflows/new-workspace.md",
+  "gsd-core/workflows/next.md",
+  "gsd-core/workflows/node-repair.md",
+  "gsd-core/workflows/note.md",
+  "gsd-core/workflows/onboard.md",
+  "gsd-core/workflows/pause-work.md",
+  "gsd-core/workflows/plan-milestone-gaps.md",
+  "gsd-core/workflows/plan-phase.md",
+  "gsd-core/workflows/plan-phase/steps/closed-phase-gate.md",
+  "gsd-core/workflows/plan-phase/steps/prd-express-path.md",
+  "gsd-core/workflows/plan-phase/steps/windows-troubleshooting.md",
+  "gsd-core/workflows/plan-review-convergence.md",
+  "gsd-core/workflows/plant-seed.md",
+  "gsd-core/workflows/pr-branch.md",
+  "gsd-core/workflows/profile-user.md",
+  "gsd-core/workflows/progress.md",
+  "gsd-core/workflows/quick.md",
+  "gsd-core/workflows/reapply-patches.md",
+  "gsd-core/workflows/remove-phase.md",
+  "gsd-core/workflows/remove-workspace.md",
+  "gsd-core/workflows/resume-project.md",
+  "gsd-core/workflows/review.md",
+  "gsd-core/workflows/scan.md",
+  "gsd-core/workflows/secure-phase.md",
+  "gsd-core/workflows/session-report.md",
+  "gsd-core/workflows/settings-advanced.md",
+  "gsd-core/workflows/settings-integrations.md",
+  "gsd-core/workflows/settings.md",
+  "gsd-core/workflows/ship.md",
+  "gsd-core/workflows/sketch-wrap-up.md",
+  "gsd-core/workflows/sketch.md",
+  "gsd-core/workflows/smart-entry.md",
+  "gsd-core/workflows/spec-phase.md",
+  "gsd-core/workflows/spike-wrap-up.md",
+  "gsd-core/workflows/spike.md",
+  "gsd-core/workflows/stats.md",
+  "gsd-core/workflows/sync-skills.md",
+  "gsd-core/workflows/thread.md",
+  "gsd-core/workflows/transition.md",
+  "gsd-core/workflows/ui-phase.md",
+  "gsd-core/workflows/ui-review.md",
+  "gsd-core/workflows/ultraplan-phase.md",
+  "gsd-core/workflows/undo.md",
+  "gsd-core/workflows/update.md",
+  "gsd-core/workflows/validate-phase.md",
+  "gsd-core/workflows/verify-phase.md",
+  "gsd-core/workflows/verify-work.md",
+  "kilo.json",
+  "plugins/gsd-core.js",
+  "scripts/changeset/README.md",
+  "scripts/changeset/cli.cjs",
+  "scripts/changeset/github-release-notes.cjs",
+  "scripts/changeset/lint.cjs",
+  "scripts/changeset/new.cjs",
+  "scripts/changeset/parse.cjs",
+  "scripts/changeset/render.cjs",
+  "scripts/changeset/serialize.cjs",
+  "scripts/fix-slash-commands.cjs",
+  "scripts/gen-capability-registry.cjs",
+  "scripts/gen-loop-host-contract.cjs",
+  "scripts/lib/allowlist-ratchet.cjs",
+  "scripts/lib/cli-exit.cjs",
+  "skills/gsd-add-tests/SKILL.md",
+  "skills/gsd-ai-integration-phase/SKILL.md",
+  "skills/gsd-audit-fix/SKILL.md",
+  "skills/gsd-audit-milestone/SKILL.md",
+  "skills/gsd-audit-uat/SKILL.md",
+  "skills/gsd-autonomous/SKILL.md",
+  "skills/gsd-capture/SKILL.md",
+  "skills/gsd-cleanup/SKILL.md",
+  "skills/gsd-code-review/SKILL.md",
+  "skills/gsd-complete-milestone/SKILL.md",
+  "skills/gsd-config/SKILL.md",
+  "skills/gsd-debug/SKILL.md",
+  "skills/gsd-discuss-phase/SKILL.md",
+  "skills/gsd-docs-update/SKILL.md",
+  "skills/gsd-eval-review/SKILL.md",
+  "skills/gsd-execute-phase/SKILL.md",
+  "skills/gsd-explore/SKILL.md",
+  "skills/gsd-extract-learnings/SKILL.md",
+  "skills/gsd-fast/SKILL.md",
+  "skills/gsd-forensics/SKILL.md",
+  "skills/gsd-graphify/SKILL.md",
+  "skills/gsd-health/SKILL.md",
+  "skills/gsd-help/SKILL.md",
+  "skills/gsd-import/SKILL.md",
+  "skills/gsd-inbox/SKILL.md",
+  "skills/gsd-ingest-docs/SKILL.md",
+  "skills/gsd-manager/SKILL.md",
+  "skills/gsd-map-codebase/SKILL.md",
+  "skills/gsd-mempalace-capture/SKILL.md",
+  "skills/gsd-mempalace-recall/SKILL.md",
+  "skills/gsd-milestone-summary/SKILL.md",
+  "skills/gsd-mvp-phase/SKILL.md",
+  "skills/gsd-new-milestone/SKILL.md",
+  "skills/gsd-new-project/SKILL.md",
+  "skills/gsd-next/SKILL.md",
+  "skills/gsd-ns-context/SKILL.md",
+  "skills/gsd-ns-ideate/SKILL.md",
+  "skills/gsd-ns-manage/SKILL.md",
+  "skills/gsd-ns-project/SKILL.md",
+  "skills/gsd-ns-review/SKILL.md",
+  "skills/gsd-ns-workflow/SKILL.md",
+  "skills/gsd-onboard/SKILL.md",
+  "skills/gsd-pause-work/SKILL.md",
+  "skills/gsd-phase/SKILL.md",
+  "skills/gsd-plan-phase/SKILL.md",
+  "skills/gsd-plan-review-convergence/SKILL.md",
+  "skills/gsd-pr-branch/SKILL.md",
+  "skills/gsd-profile-user/SKILL.md",
+  "skills/gsd-progress/SKILL.md",
+  "skills/gsd-quick/SKILL.md",
+  "skills/gsd-resume-work/SKILL.md",
+  "skills/gsd-review-backlog/SKILL.md",
+  "skills/gsd-review/SKILL.md",
+  "skills/gsd-secure-phase/SKILL.md",
+  "skills/gsd-settings/SKILL.md",
+  "skills/gsd-ship/SKILL.md",
+  "skills/gsd-sketch/SKILL.md",
+  "skills/gsd-spec-phase/SKILL.md",
+  "skills/gsd-spike/SKILL.md",
+  "skills/gsd-stats/SKILL.md",
+  "skills/gsd-surface/SKILL.md",
+  "skills/gsd-thread/SKILL.md",
+  "skills/gsd-ui-phase/SKILL.md",
+  "skills/gsd-ui-review/SKILL.md",
+  "skills/gsd-ultraplan-phase/SKILL.md",
+  "skills/gsd-undo/SKILL.md",
+  "skills/gsd-update/SKILL.md",
+  "skills/gsd-validate-phase/SKILL.md",
+  "skills/gsd-verify-work/SKILL.md",
+  "skills/gsd-workspace/SKILL.md",
+  "skills/gsd-workstreams/SKILL.md"
+]
diff --git a/tests/fixtures/install-tree/kimi.json b/tests/fixtures/install-tree/kimi.json
new file mode 100644
index 000000000..03d9428da
--- /dev/null
+++ b/tests/fixtures/install-tree/kimi.json
@@ -0,0 +1,462 @@
+[
+  ".gsd-profile",
+  ".gsd/defaults.json",
+  ".kimi/hooks/gsd-check-update-worker.js",
+  ".kimi/hooks/gsd-check-update.js",
+  ".kimi/hooks/gsd-config-reload.js",
+  ".kimi/hooks/gsd-context-monitor.js",
+  ".kimi/hooks/gsd-cursor-post-tool.js",
+  ".kimi/hooks/gsd-cursor-pre-tool.js",
+  ".kimi/hooks/gsd-cursor-session-start.js",
+  ".kimi/hooks/gsd-cursor-stop.js",
+  ".kimi/hooks/gsd-cursor-subagent-start.js",
+  ".kimi/hooks/gsd-cursor-subagent-stop.js",
+  ".kimi/hooks/gsd-ensure-canonical-path.js",
+  ".kimi/hooks/gsd-graphify-update.sh",
+  ".kimi/hooks/gsd-phase-boundary.sh",
+  ".kimi/hooks/gsd-prompt-guard.js",
+  ".kimi/hooks/gsd-read-guard.js",
+  ".kimi/hooks/gsd-read-injection-scanner.js",
+  ".kimi/hooks/gsd-session-state.sh",
+  ".kimi/hooks/gsd-statusline.js",
+  ".kimi/hooks/gsd-update-banner.js",
+  ".kimi/hooks/gsd-validate-commit.sh",
+  ".kimi/hooks/gsd-windsurf-pre-command.js",
+  ".kimi/hooks/gsd-windsurf-pre-write.js",
+  ".kimi/hooks/gsd-workflow-guard.js",
+  ".kimi/hooks/gsd-worktree-path-guard.js",
+  ".kimi/hooks/lib/git-cmd.js",
+  ".kimi/hooks/lib/gsd-graphify-rebuild.sh",
+  ".kimi/hooks/managed-hooks-registry.cjs",
+  ".kimi/package.json",
+  "agents/gsd.md",
+  "agents/gsd.yaml",
+  "agents/subagents/gsd-advisor-researcher.md",
+  "agents/subagents/gsd-advisor-researcher.yaml",
+  "agents/subagents/gsd-ai-researcher.md",
+  "agents/subagents/gsd-ai-researcher.yaml",
+  "agents/subagents/gsd-assumptions-analyzer.md",
+  "agents/subagents/gsd-assumptions-analyzer.yaml",
+  "agents/subagents/gsd-code-fixer.md",
+  "agents/subagents/gsd-code-fixer.yaml",
+  "agents/subagents/gsd-code-reviewer.md",
+  "agents/subagents/gsd-code-reviewer.yaml",
+  "agents/subagents/gsd-codebase-mapper.md",
+  "agents/subagents/gsd-codebase-mapper.yaml",
+  "agents/subagents/gsd-debug-session-manager.md",
+  "agents/subagents/gsd-debug-session-manager.yaml",
+  "agents/subagents/gsd-debugger.md",
+  "agents/subagents/gsd-debugger.yaml",
+  "agents/subagents/gsd-doc-classifier.md",
+  "agents/subagents/gsd-doc-classifier.yaml",
+  "agents/subagents/gsd-doc-synthesizer.md",
+  "agents/subagents/gsd-doc-synthesizer.yaml",
+  "agents/subagents/gsd-doc-verifier.md",
+  "agents/subagents/gsd-doc-verifier.yaml",
+  "agents/subagents/gsd-doc-writer.md",
+  "agents/subagents/gsd-doc-writer.yaml",
+  "agents/subagents/gsd-domain-researcher.md",
+  "agents/subagents/gsd-domain-researcher.yaml",
+  "agents/subagents/gsd-eval-auditor.md",
+  "agents/subagents/gsd-eval-auditor.yaml",
+  "agents/subagents/gsd-eval-planner.md",
+  "agents/subagents/gsd-eval-planner.yaml",
+  "agents/subagents/gsd-executor.md",
+  "agents/subagents/gsd-executor.yaml",
+  "agents/subagents/gsd-framework-selector.md",
+  "agents/subagents/gsd-framework-selector.yaml",
+  "agents/subagents/gsd-integration-checker.md",
+  "agents/subagents/gsd-integration-checker.yaml",
+  "agents/subagents/gsd-intel-updater.md",
+  "agents/subagents/gsd-intel-updater.yaml",
+  "agents/subagents/gsd-mempalace-curator.md",
+  "agents/subagents/gsd-mempalace-curator.yaml",
+  "agents/subagents/gsd-nyquist-auditor.md",
+  "agents/subagents/gsd-nyquist-auditor.yaml",
+  "agents/subagents/gsd-pattern-mapper.md",
+  "agents/subagents/gsd-pattern-mapper.yaml",
+  "agents/subagents/gsd-phase-researcher.md",
+  "agents/subagents/gsd-phase-researcher.yaml",
+  "agents/subagents/gsd-plan-checker.md",
+  "agents/subagents/gsd-plan-checker.yaml",
+  "agents/subagents/gsd-planner.md",
+  "agents/subagents/gsd-planner.yaml",
+  "agents/subagents/gsd-project-researcher.md",
+  "agents/subagents/gsd-project-researcher.yaml",
+  "agents/subagents/gsd-research-synthesizer.md",
+  "agents/subagents/gsd-research-synthesizer.yaml",
+  "agents/subagents/gsd-roadmapper.md",
+  "agents/subagents/gsd-roadmapper.yaml",
+  "agents/subagents/gsd-security-auditor.md",
+  "agents/subagents/gsd-security-auditor.yaml",
+  "agents/subagents/gsd-ui-auditor.md",
+  "agents/subagents/gsd-ui-auditor.yaml",
+  "agents/subagents/gsd-ui-checker.md",
+  "agents/subagents/gsd-ui-checker.yaml",
+  "agents/subagents/gsd-ui-researcher.md",
+  "agents/subagents/gsd-ui-researcher.yaml",
+  "agents/subagents/gsd-user-profiler.md",
+  "agents/subagents/gsd-user-profiler.yaml",
+  "agents/subagents/gsd-verifier.md",
+  "agents/subagents/gsd-verifier.yaml",
+  "gsd-core/VERSION",
+  "gsd-core/bin/check-latest-version.cjs",
+  "gsd-core/bin/ensure-runtime-build.cjs",
+  "gsd-core/bin/gsd-tools.cjs",
+  "gsd-core/bin/gsd_run",
+  "gsd-core/bin/shared/config-defaults.manifest.json",
+  "gsd-core/bin/shared/config-schema.manifest.json",
+  "gsd-core/bin/shared/model-catalog.json",
+  "gsd-core/bin/shared/runtime-aliases.manifest.json",
+  "gsd-core/bin/verify-reapply-patches.cjs",
+  "gsd-core/contexts/dev.md",
+  "gsd-core/contexts/research.md",
+  "gsd-core/contexts/review.md",
+  "gsd-core/references/agent-contracts.md",
+  "gsd-core/references/agent-skills-bootstrap.md",
+  "gsd-core/references/ai-evals.md",
+  "gsd-core/references/ai-frameworks.md",
+  "gsd-core/references/api-coverage.md",
+  "gsd-core/references/artifact-types.md",
+  "gsd-core/references/autonomous-smart-discuss.md",
+  "gsd-core/references/checkpoints.md",
+  "gsd-core/references/common-bug-patterns.md",
+  "gsd-core/references/context-budget.md",
+  "gsd-core/references/continuation-format.md",
+  "gsd-core/references/debugger-philosophy.md",
+  "gsd-core/references/decimal-phase-calculation.md",
+  "gsd-core/references/doc-conflict-engine.md",
+  "gsd-core/references/domain-probes.md",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/resolutions.json",
+  "gsd-core/references/edge-probe.md",
+  "gsd-core/references/execute-mvp-tdd.md",
+  "gsd-core/references/execute-phase-between-wave-reset.md",
+  "gsd-core/references/execute-phase-context-guard.md",
+  "gsd-core/references/execute-phase-wave-guard.md",
+  "gsd-core/references/executor-examples.md",
+  "gsd-core/references/few-shot-examples/plan-checker.md",
+  "gsd-core/references/few-shot-examples/verifier.md",
+  "gsd-core/references/gate-prompts.md",
+  "gsd-core/references/gates.md",
+  "gsd-core/references/git-integration.md",
+  "gsd-core/references/git-planning-commit.md",
+  "gsd-core/references/gsd-run-resolver.md",
+  "gsd-core/references/honest-verifier.md",
+  "gsd-core/references/ios-scaffold.md",
+  "gsd-core/references/loop-hook-dispatch.md",
+  "gsd-core/references/mandatory-initial-read.md",
+  "gsd-core/references/model-profile-resolution.md",
+  "gsd-core/references/model-profiles.md",
+  "gsd-core/references/mvp-concepts.md",
+  "gsd-core/references/phase-argument-parsing.md",
+  "gsd-core/references/planner-antipatterns.md",
+  "gsd-core/references/planner-chunked.md",
+  "gsd-core/references/planner-gap-closure.md",
+  "gsd-core/references/planner-graphify-auto-update.md",
+  "gsd-core/references/planner-guidance.md",
+  "gsd-core/references/planner-human-verify-mode.md",
+  "gsd-core/references/planner-interface-context.md",
+  "gsd-core/references/planner-load-graph-context.md",
+  "gsd-core/references/planner-mvp-mode.md",
+  "gsd-core/references/planner-reviews.md",
+  "gsd-core/references/planner-revision.md",
+  "gsd-core/references/planner-source-audit.md",
+  "gsd-core/references/planning-config.md",
+  "gsd-core/references/prohibition-probe-fixtures/01-streak-reminder/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/02-clean-utility/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/03-multi-prohibition/expected.json",
+  "gsd-core/references/prohibition-probe.md",
+  "gsd-core/references/project-skills-discovery.md",
+  "gsd-core/references/questioning.md",
+  "gsd-core/references/research-documentation-lookup.md",
+  "gsd-core/references/research-philosophy.md",
+  "gsd-core/references/research-verification-protocol.md",
+  "gsd-core/references/reviewer-instances.md",
+  "gsd-core/references/revision-loop.md",
+  "gsd-core/references/scout-codebase.md",
+  "gsd-core/references/security-asvs-levels.md",
+  "gsd-core/references/skeleton-template.md",
+  "gsd-core/references/sketch-interactivity.md",
+  "gsd-core/references/sketch-theme-system.md",
+  "gsd-core/references/sketch-tooling.md",
+  "gsd-core/references/sketch-variant-patterns.md",
+  "gsd-core/references/specless-probe-fallback.md",
+  "gsd-core/references/spidr-splitting.md",
+  "gsd-core/references/tdd.md",
+  "gsd-core/references/thinking-models-debug.md",
+  "gsd-core/references/thinking-models-execution.md",
+  "gsd-core/references/thinking-models-planning.md",
+  "gsd-core/references/thinking-models-research.md",
+  "gsd-core/references/thinking-models-verification.md",
+  "gsd-core/references/thinking-partner.md",
+  "gsd-core/references/ui-brand.md",
+  "gsd-core/references/ui-consideration-probe.md",
+  "gsd-core/references/universal-anti-patterns.md",
+  "gsd-core/references/untrusted-input-boundary.md",
+  "gsd-core/references/user-profiling.md",
+  "gsd-core/references/user-story-template.md",
+  "gsd-core/references/verification-overrides.md",
+  "gsd-core/references/verification-patterns.md",
+  "gsd-core/references/verify-mvp-mode.md",
+  "gsd-core/references/workstream-flag.md",
+  "gsd-core/references/worktree-branch-check.md",
+  "gsd-core/references/worktree-path-safety.md",
+  "gsd-core/templates/AI-SPEC.md",
+  "gsd-core/templates/DEBUG.md",
+  "gsd-core/templates/README.md",
+  "gsd-core/templates/SECURITY.md",
+  "gsd-core/templates/UAT.md",
+  "gsd-core/templates/UI-SPEC.md",
+  "gsd-core/templates/VALIDATION.md",
+  "gsd-core/templates/claude-md.md",
+  "gsd-core/templates/codebase/architecture.md",
+  "gsd-core/templates/codebase/concerns.md",
+  "gsd-core/templates/codebase/conventions.md",
+  "gsd-core/templates/codebase/integrations.md",
+  "gsd-core/templates/codebase/stack.md",
+  "gsd-core/templates/codebase/structure.md",
+  "gsd-core/templates/codebase/testing.md",
+  "gsd-core/templates/config.json",
+  "gsd-core/templates/context.md",
+  "gsd-core/templates/continue-here.md",
+  "gsd-core/templates/copilot-instructions.md",
+  "gsd-core/templates/debug-subagent-prompt.md",
+  "gsd-core/templates/dev-preferences.md",
+  "gsd-core/templates/discovery.md",
+  "gsd-core/templates/discussion-log.md",
+  "gsd-core/templates/milestone-archive.md",
+  "gsd-core/templates/milestone.md",
+  "gsd-core/templates/phase-prompt.md",
+  "gsd-core/templates/planner-subagent-prompt.md",
+  "gsd-core/templates/project.md",
+  "gsd-core/templates/requirements.md",
+  "gsd-core/templates/research-project/ARCHITECTURE.md",
+  "gsd-core/templates/research-project/FEATURES.md",
+  "gsd-core/templates/research-project/PITFALLS.md",
+  "gsd-core/templates/research-project/STACK.md",
+  "gsd-core/templates/research-project/SUMMARY.md",
+  "gsd-core/templates/research.md",
+  "gsd-core/templates/retrospective.md",
+  "gsd-core/templates/roadmap.md",
+  "gsd-core/templates/spec.md",
+  "gsd-core/templates/state.md",
+  "gsd-core/templates/summary-complex.md",
+  "gsd-core/templates/summary-minimal.md",
+  "gsd-core/templates/summary-standard.md",
+  "gsd-core/templates/summary.md",
+  "gsd-core/templates/user-profile.md",
+  "gsd-core/templates/user-setup.md",
+  "gsd-core/templates/verification-report.md",
+  "gsd-core/workflows/_runtime-launcher.snippet.sh",
+  "gsd-core/workflows/add-backlog.md",
+  "gsd-core/workflows/add-phase.md",
+  "gsd-core/workflows/add-tests.md",
+  "gsd-core/workflows/add-todo.md",
+  "gsd-core/workflows/ai-integration-phase.md",
+  "gsd-core/workflows/analyze-dependencies.md",
+  "gsd-core/workflows/audit-fix.md",
+  "gsd-core/workflows/audit-milestone.md",
+  "gsd-core/workflows/audit-uat.md",
+  "gsd-core/workflows/autonomous.md",
+  "gsd-core/workflows/check-todos.md",
+  "gsd-core/workflows/cleanup.md",
+  "gsd-core/workflows/code-review-fix.md",
+  "gsd-core/workflows/code-review.md",
+  "gsd-core/workflows/complete-milestone.md",
+  "gsd-core/workflows/debug.md",
+  "gsd-core/workflows/diagnose-issues.md",
+  "gsd-core/workflows/discovery-phase.md",
+  "gsd-core/workflows/discuss-phase-assumptions.md",
+  "gsd-core/workflows/discuss-phase-power.md",
+  "gsd-core/workflows/discuss-phase.md",
+  "gsd-core/workflows/discuss-phase/modes/advisor.md",
+  "gsd-core/workflows/discuss-phase/modes/all.md",
+  "gsd-core/workflows/discuss-phase/modes/analyze.md",
+  "gsd-core/workflows/discuss-phase/modes/auto.md",
+  "gsd-core/workflows/discuss-phase/modes/batch.md",
+  "gsd-core/workflows/discuss-phase/modes/chain.md",
+  "gsd-core/workflows/discuss-phase/modes/default.md",
+  "gsd-core/workflows/discuss-phase/modes/power.md",
+  "gsd-core/workflows/discuss-phase/modes/text.md",
+  "gsd-core/workflows/discuss-phase/templates/checkpoint.json",
+  "gsd-core/workflows/discuss-phase/templates/context.md",
+  "gsd-core/workflows/discuss-phase/templates/discussion-log.md",
+  "gsd-core/workflows/do.md",
+  "gsd-core/workflows/docs-update.md",
+  "gsd-core/workflows/edit-phase.md",
+  "gsd-core/workflows/eval-review.md",
+  "gsd-core/workflows/execute-phase.md",
+  "gsd-core/workflows/execute-phase/steps/codebase-drift-gate.md",
+  "gsd-core/workflows/execute-phase/steps/per-plan-worktree-gate.md",
+  "gsd-core/workflows/execute-phase/steps/post-merge-gate.md",
+  "gsd-core/workflows/execute-phase/steps/regression-gate.md",
+  "gsd-core/workflows/execute-phase/steps/worktree-recovery-policy.md",
+  "gsd-core/workflows/execute-plan.md",
+  "gsd-core/workflows/explore.md",
+  "gsd-core/workflows/extract-learnings.md",
+  "gsd-core/workflows/fast.md",
+  "gsd-core/workflows/forensics.md",
+  "gsd-core/workflows/graduation.md",
+  "gsd-core/workflows/health.md",
+  "gsd-core/workflows/help.md",
+  "gsd-core/workflows/help/modes/brief.md",
+  "gsd-core/workflows/help/modes/default.md",
+  "gsd-core/workflows/help/modes/full.md",
+  "gsd-core/workflows/help/modes/topic.md",
+  "gsd-core/workflows/import.md",
+  "gsd-core/workflows/inbox.md",
+  "gsd-core/workflows/ingest-docs.md",
+  "gsd-core/workflows/insert-phase.md",
+  "gsd-core/workflows/list-phase-assumptions.md",
+  "gsd-core/workflows/list-seeds.md",
+  "gsd-core/workflows/list-workspaces.md",
+  "gsd-core/workflows/manager.md",
+  "gsd-core/workflows/map-codebase.md",
+  "gsd-core/workflows/milestone-summary.md",
+  "gsd-core/workflows/mvp-phase.md",
+  "gsd-core/workflows/new-milestone.md",
+  "gsd-core/workflows/new-project.md",
+  "gsd-core/workflows/new-workspace.md",
+  "gsd-core/workflows/next.md",
+  "gsd-core/workflows/node-repair.md",
+  "gsd-core/workflows/note.md",
+  "gsd-core/workflows/onboard.md",
+  "gsd-core/workflows/pause-work.md",
+  "gsd-core/workflows/plan-milestone-gaps.md",
+  "gsd-core/workflows/plan-phase.md",
+  "gsd-core/workflows/plan-phase/steps/closed-phase-gate.md",
+  "gsd-core/workflows/plan-phase/steps/prd-express-path.md",
+  "gsd-core/workflows/plan-phase/steps/windows-troubleshooting.md",
+  "gsd-core/workflows/plan-review-convergence.md",
+  "gsd-core/workflows/plant-seed.md",
+  "gsd-core/workflows/pr-branch.md",
+  "gsd-core/workflows/profile-user.md",
+  "gsd-core/workflows/progress.md",
+  "gsd-core/workflows/quick.md",
+  "gsd-core/workflows/reapply-patches.md",
+  "gsd-core/workflows/remove-phase.md",
+  "gsd-core/workflows/remove-workspace.md",
+  "gsd-core/workflows/resume-project.md",
+  "gsd-core/workflows/review.md",
+  "gsd-core/workflows/scan.md",
+  "gsd-core/workflows/secure-phase.md",
+  "gsd-core/workflows/session-report.md",
+  "gsd-core/workflows/settings-advanced.md",
+  "gsd-core/workflows/settings-integrations.md",
+  "gsd-core/workflows/settings.md",
+  "gsd-core/workflows/ship.md",
+  "gsd-core/workflows/sketch-wrap-up.md",
+  "gsd-core/workflows/sketch.md",
+  "gsd-core/workflows/smart-entry.md",
+  "gsd-core/workflows/spec-phase.md",
+  "gsd-core/workflows/spike-wrap-up.md",
+  "gsd-core/workflows/spike.md",
+  "gsd-core/workflows/stats.md",
+  "gsd-core/workflows/sync-skills.md",
+  "gsd-core/workflows/thread.md",
+  "gsd-core/workflows/transition.md",
+  "gsd-core/workflows/ui-phase.md",
+  "gsd-core/workflows/ui-review.md",
+  "gsd-core/workflows/ultraplan-phase.md",
+  "gsd-core/workflows/undo.md",
+  "gsd-core/workflows/update.md",
+  "gsd-core/workflows/validate-phase.md",
+  "gsd-core/workflows/verify-phase.md",
+  "gsd-core/workflows/verify-work.md",
+  "scripts/changeset/README.md",
+  "scripts/changeset/cli.cjs",
+  "scripts/changeset/github-release-notes.cjs",
+  "scripts/changeset/lint.cjs",
+  "scripts/changeset/new.cjs",
+  "scripts/changeset/parse.cjs",
+  "scripts/changeset/render.cjs",
+  "scripts/changeset/serialize.cjs",
+  "scripts/fix-slash-commands.cjs",
+  "scripts/gen-capability-registry.cjs",
+  "scripts/gen-loop-host-contract.cjs",
+  "scripts/lib/allowlist-ratchet.cjs",
+  "scripts/lib/cli-exit.cjs",
+  "skills/gsd-add-tests/SKILL.md",
+  "skills/gsd-ai-integration-phase/SKILL.md",
+  "skills/gsd-audit-fix/SKILL.md",
+  "skills/gsd-audit-milestone/SKILL.md",
+  "skills/gsd-audit-uat/SKILL.md",
+  "skills/gsd-autonomous/SKILL.md",
+  "skills/gsd-capture/SKILL.md",
+  "skills/gsd-cleanup/SKILL.md",
+  "skills/gsd-code-review/SKILL.md",
+  "skills/gsd-complete-milestone/SKILL.md",
+  "skills/gsd-config/SKILL.md",
+  "skills/gsd-debug/SKILL.md",
+  "skills/gsd-discuss-phase/SKILL.md",
+  "skills/gsd-docs-update/SKILL.md",
+  "skills/gsd-eval-review/SKILL.md",
+  "skills/gsd-execute-phase/SKILL.md",
+  "skills/gsd-explore/SKILL.md",
+  "skills/gsd-extract-learnings/SKILL.md",
+  "skills/gsd-fast/SKILL.md",
+  "skills/gsd-forensics/SKILL.md",
+  "skills/gsd-graphify/SKILL.md",
+  "skills/gsd-health/SKILL.md",
+  "skills/gsd-help/SKILL.md",
+  "skills/gsd-import/SKILL.md",
+  "skills/gsd-inbox/SKILL.md",
+  "skills/gsd-ingest-docs/SKILL.md",
+  "skills/gsd-manager/SKILL.md",
+  "skills/gsd-map-codebase/SKILL.md",
+  "skills/gsd-mempalace-capture/SKILL.md",
+  "skills/gsd-mempalace-recall/SKILL.md",
+  "skills/gsd-milestone-summary/SKILL.md",
+  "skills/gsd-mvp-phase/SKILL.md",
+  "skills/gsd-new-milestone/SKILL.md",
+  "skills/gsd-new-project/SKILL.md",
+  "skills/gsd-next/SKILL.md",
+  "skills/gsd-ns-context/SKILL.md",
+  "skills/gsd-ns-ideate/SKILL.md",
+  "skills/gsd-ns-manage/SKILL.md",
+  "skills/gsd-ns-project/SKILL.md",
+  "skills/gsd-ns-review/SKILL.md",
+  "skills/gsd-ns-workflow/SKILL.md",
+  "skills/gsd-onboard/SKILL.md",
+  "skills/gsd-pause-work/SKILL.md",
+  "skills/gsd-phase/SKILL.md",
+  "skills/gsd-plan-phase/SKILL.md",
+  "skills/gsd-plan-review-convergence/SKILL.md",
+  "skills/gsd-pr-branch/SKILL.md",
+  "skills/gsd-profile-user/SKILL.md",
+  "skills/gsd-progress/SKILL.md",
+  "skills/gsd-quick/SKILL.md",
+  "skills/gsd-resume-work/SKILL.md",
+  "skills/gsd-review-backlog/SKILL.md",
+  "skills/gsd-review/SKILL.md",
+  "skills/gsd-secure-phase/SKILL.md",
+  "skills/gsd-settings/SKILL.md",
+  "skills/gsd-ship/SKILL.md",
+  "skills/gsd-sketch/SKILL.md",
+  "skills/gsd-spec-phase/SKILL.md",
+  "skills/gsd-spike/SKILL.md",
+  "skills/gsd-stats/SKILL.md",
+  "skills/gsd-surface/SKILL.md",
+  "skills/gsd-thread/SKILL.md",
+  "skills/gsd-ui-phase/SKILL.md",
+  "skills/gsd-ui-review/SKILL.md",
+  "skills/gsd-ultraplan-phase/SKILL.md",
+  "skills/gsd-undo/SKILL.md",
+  "skills/gsd-update/SKILL.md",
+  "skills/gsd-validate-phase/SKILL.md",
+  "skills/gsd-verify-work/SKILL.md",
+  "skills/gsd-workspace/SKILL.md",
+  "skills/gsd-workstreams/SKILL.md"
+]
diff --git a/tests/fixtures/install-tree/opencode.json b/tests/fixtures/install-tree/opencode.json
new file mode 100644
index 000000000..0ac467bf3
--- /dev/null
+++ b/tests/fixtures/install-tree/opencode.json
@@ -0,0 +1,499 @@
+[
+  ".gsd-profile",
+  ".gsd/defaults.json",
+  "agents/gsd-advisor-researcher.md",
+  "agents/gsd-ai-researcher.md",
+  "agents/gsd-assumptions-analyzer.md",
+  "agents/gsd-code-fixer.md",
+  "agents/gsd-code-reviewer.md",
+  "agents/gsd-codebase-mapper.md",
+  "agents/gsd-debug-session-manager.md",
+  "agents/gsd-debugger.md",
+  "agents/gsd-doc-classifier.md",
+  "agents/gsd-doc-synthesizer.md",
+  "agents/gsd-doc-verifier.md",
+  "agents/gsd-doc-writer.md",
+  "agents/gsd-domain-researcher.md",
+  "agents/gsd-eval-auditor.md",
+  "agents/gsd-eval-planner.md",
+  "agents/gsd-executor.md",
+  "agents/gsd-framework-selector.md",
+  "agents/gsd-integration-checker.md",
+  "agents/gsd-intel-updater.md",
+  "agents/gsd-mempalace-curator.md",
+  "agents/gsd-nyquist-auditor.md",
+  "agents/gsd-pattern-mapper.md",
+  "agents/gsd-phase-researcher.md",
+  "agents/gsd-plan-checker.md",
+  "agents/gsd-planner.md",
+  "agents/gsd-project-researcher.md",
+  "agents/gsd-research-synthesizer.md",
+  "agents/gsd-roadmapper.md",
+  "agents/gsd-security-auditor.md",
+  "agents/gsd-ui-auditor.md",
+  "agents/gsd-ui-checker.md",
+  "agents/gsd-ui-researcher.md",
+  "agents/gsd-user-profiler.md",
+  "agents/gsd-verifier.md",
+  "command/gsd-add-tests.md",
+  "command/gsd-ai-integration-phase.md",
+  "command/gsd-audit-fix.md",
+  "command/gsd-audit-milestone.md",
+  "command/gsd-audit-uat.md",
+  "command/gsd-autonomous.md",
+  "command/gsd-capture.md",
+  "command/gsd-cleanup.md",
+  "command/gsd-code-review.md",
+  "command/gsd-complete-milestone.md",
+  "command/gsd-config.md",
+  "command/gsd-debug.md",
+  "command/gsd-discuss-phase.md",
+  "command/gsd-docs-update.md",
+  "command/gsd-eval-review.md",
+  "command/gsd-execute-phase.md",
+  "command/gsd-explore.md",
+  "command/gsd-extract-learnings.md",
+  "command/gsd-fast.md",
+  "command/gsd-forensics.md",
+  "command/gsd-graphify.md",
+  "command/gsd-health.md",
+  "command/gsd-help.md",
+  "command/gsd-import.md",
+  "command/gsd-inbox.md",
+  "command/gsd-ingest-docs.md",
+  "command/gsd-manager.md",
+  "command/gsd-map-codebase.md",
+  "command/gsd-mempalace-capture.md",
+  "command/gsd-mempalace-recall.md",
+  "command/gsd-milestone-summary.md",
+  "command/gsd-mvp-phase.md",
+  "command/gsd-new-milestone.md",
+  "command/gsd-new-project.md",
+  "command/gsd-next.md",
+  "command/gsd-ns-context.md",
+  "command/gsd-ns-ideate.md",
+  "command/gsd-ns-manage.md",
+  "command/gsd-ns-project.md",
+  "command/gsd-ns-review.md",
+  "command/gsd-ns-workflow.md",
+  "command/gsd-onboard.md",
+  "command/gsd-pause-work.md",
+  "command/gsd-phase.md",
+  "command/gsd-plan-phase.md",
+  "command/gsd-plan-review-convergence.md",
+  "command/gsd-pr-branch.md",
+  "command/gsd-profile-user.md",
+  "command/gsd-progress.md",
+  "command/gsd-quick.md",
+  "command/gsd-resume-work.md",
+  "command/gsd-review-backlog.md",
+  "command/gsd-review.md",
+  "command/gsd-secure-phase.md",
+  "command/gsd-settings.md",
+  "command/gsd-ship.md",
+  "command/gsd-sketch.md",
+  "command/gsd-spec-phase.md",
+  "command/gsd-spike.md",
+  "command/gsd-stats.md",
+  "command/gsd-surface.md",
+  "command/gsd-thread.md",
+  "command/gsd-ui-phase.md",
+  "command/gsd-ui-review.md",
+  "command/gsd-ultraplan-phase.md",
+  "command/gsd-undo.md",
+  "command/gsd-update.md",
+  "command/gsd-validate-phase.md",
+  "command/gsd-verify-work.md",
+  "command/gsd-workspace.md",
+  "command/gsd-workstreams.md",
+  "gsd-core/VERSION",
+  "gsd-core/bin/check-latest-version.cjs",
+  "gsd-core/bin/ensure-runtime-build.cjs",
+  "gsd-core/bin/gsd-tools.cjs",
+  "gsd-core/bin/gsd_run",
+  "gsd-core/bin/shared/config-defaults.manifest.json",
+  "gsd-core/bin/shared/config-schema.manifest.json",
+  "gsd-core/bin/shared/model-catalog.json",
+  "gsd-core/bin/shared/runtime-aliases.manifest.json",
+  "gsd-core/bin/verify-reapply-patches.cjs",
+  "gsd-core/contexts/dev.md",
+  "gsd-core/contexts/research.md",
+  "gsd-core/contexts/review.md",
+  "gsd-core/references/agent-contracts.md",
+  "gsd-core/references/agent-skills-bootstrap.md",
+  "gsd-core/references/ai-evals.md",
+  "gsd-core/references/ai-frameworks.md",
+  "gsd-core/references/api-coverage.md",
+  "gsd-core/references/artifact-types.md",
+  "gsd-core/references/autonomous-smart-discuss.md",
+  "gsd-core/references/checkpoints.md",
+  "gsd-core/references/common-bug-patterns.md",
+  "gsd-core/references/context-budget.md",
+  "gsd-core/references/continuation-format.md",
+  "gsd-core/references/debugger-philosophy.md",
+  "gsd-core/references/decimal-phase-calculation.md",
+  "gsd-core/references/doc-conflict-engine.md",
+  "gsd-core/references/domain-probes.md",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/resolutions.json",
+  "gsd-core/references/edge-probe.md",
+  "gsd-core/references/execute-mvp-tdd.md",
+  "gsd-core/references/execute-phase-between-wave-reset.md",
+  "gsd-core/references/execute-phase-context-guard.md",
+  "gsd-core/references/execute-phase-wave-guard.md",
+  "gsd-core/references/executor-examples.md",
+  "gsd-core/references/few-shot-examples/plan-checker.md",
+  "gsd-core/references/few-shot-examples/verifier.md",
+  "gsd-core/references/gate-prompts.md",
+  "gsd-core/references/gates.md",
+  "gsd-core/references/git-integration.md",
+  "gsd-core/references/git-planning-commit.md",
+  "gsd-core/references/gsd-run-resolver.md",
+  "gsd-core/references/honest-verifier.md",
+  "gsd-core/references/ios-scaffold.md",
+  "gsd-core/references/loop-hook-dispatch.md",
+  "gsd-core/references/mandatory-initial-read.md",
+  "gsd-core/references/model-profile-resolution.md",
+  "gsd-core/references/model-profiles.md",
+  "gsd-core/references/mvp-concepts.md",
+  "gsd-core/references/phase-argument-parsing.md",
+  "gsd-core/references/planner-antipatterns.md",
+  "gsd-core/references/planner-chunked.md",
+  "gsd-core/references/planner-gap-closure.md",
+  "gsd-core/references/planner-graphify-auto-update.md",
+  "gsd-core/references/planner-guidance.md",
+  "gsd-core/references/planner-human-verify-mode.md",
+  "gsd-core/references/planner-interface-context.md",
+  "gsd-core/references/planner-load-graph-context.md",
+  "gsd-core/references/planner-mvp-mode.md",
+  "gsd-core/references/planner-reviews.md",
+  "gsd-core/references/planner-revision.md",
+  "gsd-core/references/planner-source-audit.md",
+  "gsd-core/references/planning-config.md",
+  "gsd-core/references/prohibition-probe-fixtures/01-streak-reminder/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/02-clean-utility/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/03-multi-prohibition/expected.json",
+  "gsd-core/references/prohibition-probe.md",
+  "gsd-core/references/project-skills-discovery.md",
+  "gsd-core/references/questioning.md",
+  "gsd-core/references/research-documentation-lookup.md",
+  "gsd-core/references/research-philosophy.md",
+  "gsd-core/references/research-verification-protocol.md",
+  "gsd-core/references/reviewer-instances.md",
+  "gsd-core/references/revision-loop.md",
+  "gsd-core/references/scout-codebase.md",
+  "gsd-core/references/security-asvs-levels.md",
+  "gsd-core/references/skeleton-template.md",
+  "gsd-core/references/sketch-interactivity.md",
+  "gsd-core/references/sketch-theme-system.md",
+  "gsd-core/references/sketch-tooling.md",
+  "gsd-core/references/sketch-variant-patterns.md",
+  "gsd-core/references/specless-probe-fallback.md",
+  "gsd-core/references/spidr-splitting.md",
+  "gsd-core/references/tdd.md",
+  "gsd-core/references/thinking-models-debug.md",
+  "gsd-core/references/thinking-models-execution.md",
+  "gsd-core/references/thinking-models-planning.md",
+  "gsd-core/references/thinking-models-research.md",
+  "gsd-core/references/thinking-models-verification.md",
+  "gsd-core/references/thinking-partner.md",
+  "gsd-core/references/ui-brand.md",
+  "gsd-core/references/ui-consideration-probe.md",
+  "gsd-core/references/universal-anti-patterns.md",
+  "gsd-core/references/untrusted-input-boundary.md",
+  "gsd-core/references/user-profiling.md",
+  "gsd-core/references/user-story-template.md",
+  "gsd-core/references/verification-overrides.md",
+  "gsd-core/references/verification-patterns.md",
+  "gsd-core/references/verify-mvp-mode.md",
+  "gsd-core/references/workstream-flag.md",
+  "gsd-core/references/worktree-branch-check.md",
+  "gsd-core/references/worktree-path-safety.md",
+  "gsd-core/templates/AI-SPEC.md",
+  "gsd-core/templates/DEBUG.md",
+  "gsd-core/templates/README.md",
+  "gsd-core/templates/SECURITY.md",
+  "gsd-core/templates/UAT.md",
+  "gsd-core/templates/UI-SPEC.md",
+  "gsd-core/templates/VALIDATION.md",
+  "gsd-core/templates/claude-md.md",
+  "gsd-core/templates/codebase/architecture.md",
+  "gsd-core/templates/codebase/concerns.md",
+  "gsd-core/templates/codebase/conventions.md",
+  "gsd-core/templates/codebase/integrations.md",
+  "gsd-core/templates/codebase/stack.md",
+  "gsd-core/templates/codebase/structure.md",
+  "gsd-core/templates/codebase/testing.md",
+  "gsd-core/templates/config.json",
+  "gsd-core/templates/context.md",
+  "gsd-core/templates/continue-here.md",
+  "gsd-core/templates/copilot-instructions.md",
+  "gsd-core/templates/debug-subagent-prompt.md",
+  "gsd-core/templates/dev-preferences.md",
+  "gsd-core/templates/discovery.md",
+  "gsd-core/templates/discussion-log.md",
+  "gsd-core/templates/milestone-archive.md",
+  "gsd-core/templates/milestone.md",
+  "gsd-core/templates/phase-prompt.md",
+  "gsd-core/templates/planner-subagent-prompt.md",
+  "gsd-core/templates/project.md",
+  "gsd-core/templates/requirements.md",
+  "gsd-core/templates/research-project/ARCHITECTURE.md",
+  "gsd-core/templates/research-project/FEATURES.md",
+  "gsd-core/templates/research-project/PITFALLS.md",
+  "gsd-core/templates/research-project/STACK.md",
+  "gsd-core/templates/research-project/SUMMARY.md",
+  "gsd-core/templates/research.md",
+  "gsd-core/templates/retrospective.md",
+  "gsd-core/templates/roadmap.md",
+  "gsd-core/templates/spec.md",
+  "gsd-core/templates/state.md",
+  "gsd-core/templates/summary-complex.md",
+  "gsd-core/templates/summary-minimal.md",
+  "gsd-core/templates/summary-standard.md",
+  "gsd-core/templates/summary.md",
+  "gsd-core/templates/user-profile.md",
+  "gsd-core/templates/user-setup.md",
+  "gsd-core/templates/verification-report.md",
+  "gsd-core/workflows/_runtime-launcher.snippet.sh",
+  "gsd-core/workflows/add-backlog.md",
+  "gsd-core/workflows/add-phase.md",
+  "gsd-core/workflows/add-tests.md",
+  "gsd-core/workflows/add-todo.md",
+  "gsd-core/workflows/ai-integration-phase.md",
+  "gsd-core/workflows/analyze-dependencies.md",
+  "gsd-core/workflows/audit-fix.md",
+  "gsd-core/workflows/audit-milestone.md",
+  "gsd-core/workflows/audit-uat.md",
+  "gsd-core/workflows/autonomous.md",
+  "gsd-core/workflows/check-todos.md",
+  "gsd-core/workflows/cleanup.md",
+  "gsd-core/workflows/code-review-fix.md",
+  "gsd-core/workflows/code-review.md",
+  "gsd-core/workflows/complete-milestone.md",
+  "gsd-core/workflows/debug.md",
+  "gsd-core/workflows/diagnose-issues.md",
+  "gsd-core/workflows/discovery-phase.md",
+  "gsd-core/workflows/discuss-phase-assumptions.md",
+  "gsd-core/workflows/discuss-phase-power.md",
+  "gsd-core/workflows/discuss-phase.md",
+  "gsd-core/workflows/discuss-phase/modes/advisor.md",
+  "gsd-core/workflows/discuss-phase/modes/all.md",
+  "gsd-core/workflows/discuss-phase/modes/analyze.md",
+  "gsd-core/workflows/discuss-phase/modes/auto.md",
+  "gsd-core/workflows/discuss-phase/modes/batch.md",
+  "gsd-core/workflows/discuss-phase/modes/chain.md",
+  "gsd-core/workflows/discuss-phase/modes/default.md",
+  "gsd-core/workflows/discuss-phase/modes/power.md",
+  "gsd-core/workflows/discuss-phase/modes/text.md",
+  "gsd-core/workflows/discuss-phase/templates/checkpoint.json",
+  "gsd-core/workflows/discuss-phase/templates/context.md",
+  "gsd-core/workflows/discuss-phase/templates/discussion-log.md",
+  "gsd-core/workflows/do.md",
+  "gsd-core/workflows/docs-update.md",
+  "gsd-core/workflows/edit-phase.md",
+  "gsd-core/workflows/eval-review.md",
+  "gsd-core/workflows/execute-phase.md",
+  "gsd-core/workflows/execute-phase/steps/codebase-drift-gate.md",
+  "gsd-core/workflows/execute-phase/steps/per-plan-worktree-gate.md",
+  "gsd-core/workflows/execute-phase/steps/post-merge-gate.md",
+  "gsd-core/workflows/execute-phase/steps/regression-gate.md",
+  "gsd-core/workflows/execute-phase/steps/worktree-recovery-policy.md",
+  "gsd-core/workflows/execute-plan.md",
+  "gsd-core/workflows/explore.md",
+  "gsd-core/workflows/extract-learnings.md",
+  "gsd-core/workflows/fast.md",
+  "gsd-core/workflows/forensics.md",
+  "gsd-core/workflows/graduation.md",
+  "gsd-core/workflows/health.md",
+  "gsd-core/workflows/help.md",
+  "gsd-core/workflows/help/modes/brief.md",
+  "gsd-core/workflows/help/modes/default.md",
+  "gsd-core/workflows/help/modes/full.md",
+  "gsd-core/workflows/help/modes/topic.md",
+  "gsd-core/workflows/import.md",
+  "gsd-core/workflows/inbox.md",
+  "gsd-core/workflows/ingest-docs.md",
+  "gsd-core/workflows/insert-phase.md",
+  "gsd-core/workflows/list-phase-assumptions.md",
+  "gsd-core/workflows/list-seeds.md",
+  "gsd-core/workflows/list-workspaces.md",
+  "gsd-core/workflows/manager.md",
+  "gsd-core/workflows/map-codebase.md",
+  "gsd-core/workflows/milestone-summary.md",
+  "gsd-core/workflows/mvp-phase.md",
+  "gsd-core/workflows/new-milestone.md",
+  "gsd-core/workflows/new-project.md",
+  "gsd-core/workflows/new-workspace.md",
+  "gsd-core/workflows/next.md",
+  "gsd-core/workflows/node-repair.md",
+  "gsd-core/workflows/note.md",
+  "gsd-core/workflows/onboard.md",
+  "gsd-core/workflows/pause-work.md",
+  "gsd-core/workflows/plan-milestone-gaps.md",
+  "gsd-core/workflows/plan-phase.md",
+  "gsd-core/workflows/plan-phase/steps/closed-phase-gate.md",
+  "gsd-core/workflows/plan-phase/steps/prd-express-path.md",
+  "gsd-core/workflows/plan-phase/steps/windows-troubleshooting.md",
+  "gsd-core/workflows/plan-review-convergence.md",
+  "gsd-core/workflows/plant-seed.md",
+  "gsd-core/workflows/pr-branch.md",
+  "gsd-core/workflows/profile-user.md",
+  "gsd-core/workflows/progress.md",
+  "gsd-core/workflows/quick.md",
+  "gsd-core/workflows/reapply-patches.md",
+  "gsd-core/workflows/remove-phase.md",
+  "gsd-core/workflows/remove-workspace.md",
+  "gsd-core/workflows/resume-project.md",
+  "gsd-core/workflows/review.md",
+  "gsd-core/workflows/scan.md",
+  "gsd-core/workflows/secure-phase.md",
+  "gsd-core/workflows/session-report.md",
+  "gsd-core/workflows/settings-advanced.md",
+  "gsd-core/workflows/settings-integrations.md",
+  "gsd-core/workflows/settings.md",
+  "gsd-core/workflows/ship.md",
+  "gsd-core/workflows/sketch-wrap-up.md",
+  "gsd-core/workflows/sketch.md",
+  "gsd-core/workflows/smart-entry.md",
+  "gsd-core/workflows/spec-phase.md",
+  "gsd-core/workflows/spike-wrap-up.md",
+  "gsd-core/workflows/spike.md",
+  "gsd-core/workflows/stats.md",
+  "gsd-core/workflows/sync-skills.md",
+  "gsd-core/workflows/thread.md",
+  "gsd-core/workflows/transition.md",
+  "gsd-core/workflows/ui-phase.md",
+  "gsd-core/workflows/ui-review.md",
+  "gsd-core/workflows/ultraplan-phase.md",
+  "gsd-core/workflows/undo.md",
+  "gsd-core/workflows/update.md",
+  "gsd-core/workflows/validate-phase.md",
+  "gsd-core/workflows/verify-phase.md",
+  "gsd-core/workflows/verify-work.md",
+  "hooks/gsd-check-update-worker.js",
+  "hooks/gsd-check-update.js",
+  "hooks/gsd-config-reload.js",
+  "hooks/gsd-context-monitor.js",
+  "hooks/gsd-cursor-post-tool.js",
+  "hooks/gsd-cursor-pre-tool.js",
+  "hooks/gsd-cursor-session-start.js",
+  "hooks/gsd-cursor-stop.js",
+  "hooks/gsd-cursor-subagent-start.js",
+  "hooks/gsd-cursor-subagent-stop.js",
+  "hooks/gsd-ensure-canonical-path.js",
+  "hooks/gsd-graphify-update.sh",
+  "hooks/gsd-phase-boundary.sh",
+  "hooks/gsd-prompt-guard.js",
+  "hooks/gsd-read-guard.js",
+  "hooks/gsd-read-injection-scanner.js",
+  "hooks/gsd-session-state.sh",
+  "hooks/gsd-statusline.js",
+  "hooks/gsd-update-banner.js",
+  "hooks/gsd-validate-commit.sh",
+  "hooks/gsd-windsurf-pre-command.js",
+  "hooks/gsd-windsurf-pre-write.js",
+  "hooks/gsd-workflow-guard.js",
+  "hooks/gsd-worktree-path-guard.js",
+  "hooks/lib/git-cmd.js",
+  "hooks/lib/gsd-graphify-rebuild.sh",
+  "hooks/managed-hooks-registry.cjs",
+  "opencode.json",
+  "package.json",
+  "plugins/gsd-core.js",
+  "scripts/changeset/README.md",
+  "scripts/changeset/cli.cjs",
+  "scripts/changeset/github-release-notes.cjs",
+  "scripts/changeset/lint.cjs",
+  "scripts/changeset/new.cjs",
+  "scripts/changeset/parse.cjs",
+  "scripts/changeset/render.cjs",
+  "scripts/changeset/serialize.cjs",
+  "scripts/fix-slash-commands.cjs",
+  "scripts/gen-capability-registry.cjs",
+  "scripts/gen-loop-host-contract.cjs",
+  "scripts/lib/allowlist-ratchet.cjs",
+  "scripts/lib/cli-exit.cjs",
+  "skills/gsd-add-tests/SKILL.md",
+  "skills/gsd-ai-integration-phase/SKILL.md",
+  "skills/gsd-audit-fix/SKILL.md",
+  "skills/gsd-audit-milestone/SKILL.md",
+  "skills/gsd-audit-uat/SKILL.md",
+  "skills/gsd-autonomous/SKILL.md",
+  "skills/gsd-capture/SKILL.md",
+  "skills/gsd-cleanup/SKILL.md",
+  "skills/gsd-code-review/SKILL.md",
+  "skills/gsd-complete-milestone/SKILL.md",
+  "skills/gsd-config/SKILL.md",
+  "skills/gsd-debug/SKILL.md",
+  "skills/gsd-discuss-phase/SKILL.md",
+  "skills/gsd-docs-update/SKILL.md",
+  "skills/gsd-eval-review/SKILL.md",
+  "skills/gsd-execute-phase/SKILL.md",
+  "skills/gsd-explore/SKILL.md",
+  "skills/gsd-extract-learnings/SKILL.md",
+  "skills/gsd-fast/SKILL.md",
+  "skills/gsd-forensics/SKILL.md",
+  "skills/gsd-graphify/SKILL.md",
+  "skills/gsd-health/SKILL.md",
+  "skills/gsd-help/SKILL.md",
+  "skills/gsd-import/SKILL.md",
+  "skills/gsd-inbox/SKILL.md",
+  "skills/gsd-ingest-docs/SKILL.md",
+  "skills/gsd-manager/SKILL.md",
+  "skills/gsd-map-codebase/SKILL.md",
+  "skills/gsd-mempalace-capture/SKILL.md",
+  "skills/gsd-mempalace-recall/SKILL.md",
+  "skills/gsd-milestone-summary/SKILL.md",
+  "skills/gsd-mvp-phase/SKILL.md",
+  "skills/gsd-new-milestone/SKILL.md",
+  "skills/gsd-new-project/SKILL.md",
+  "skills/gsd-next/SKILL.md",
+  "skills/gsd-ns-context/SKILL.md",
+  "skills/gsd-ns-ideate/SKILL.md",
+  "skills/gsd-ns-manage/SKILL.md",
+  "skills/gsd-ns-project/SKILL.md",
+  "skills/gsd-ns-review/SKILL.md",
+  "skills/gsd-ns-workflow/SKILL.md",
+  "skills/gsd-onboard/SKILL.md",
+  "skills/gsd-pause-work/SKILL.md",
+  "skills/gsd-phase/SKILL.md",
+  "skills/gsd-plan-phase/SKILL.md",
+  "skills/gsd-plan-review-convergence/SKILL.md",
+  "skills/gsd-pr-branch/SKILL.md",
+  "skills/gsd-profile-user/SKILL.md",
+  "skills/gsd-progress/SKILL.md",
+  "skills/gsd-quick/SKILL.md",
+  "skills/gsd-resume-work/SKILL.md",
+  "skills/gsd-review-backlog/SKILL.md",
+  "skills/gsd-review/SKILL.md",
+  "skills/gsd-secure-phase/SKILL.md",
+  "skills/gsd-settings/SKILL.md",
+  "skills/gsd-ship/SKILL.md",
+  "skills/gsd-sketch/SKILL.md",
+  "skills/gsd-spec-phase/SKILL.md",
+  "skills/gsd-spike/SKILL.md",
+  "skills/gsd-stats/SKILL.md",
+  "skills/gsd-surface/SKILL.md",
+  "skills/gsd-thread/SKILL.md",
+  "skills/gsd-ui-phase/SKILL.md",
+  "skills/gsd-ui-review/SKILL.md",
+  "skills/gsd-ultraplan-phase/SKILL.md",
+  "skills/gsd-undo/SKILL.md",
+  "skills/gsd-update/SKILL.md",
+  "skills/gsd-validate-phase/SKILL.md",
+  "skills/gsd-verify-work/SKILL.md",
+  "skills/gsd-workspace/SKILL.md",
+  "skills/gsd-workstreams/SKILL.md"
+]
diff --git a/tests/fixtures/install-tree/pi.json b/tests/fixtures/install-tree/pi.json
new file mode 100644
index 000000000..31f35703b
--- /dev/null
+++ b/tests/fixtures/install-tree/pi.json
@@ -0,0 +1,322 @@
+[
+  ".gsd-profile",
+  ".gsd/defaults.json",
+  "extensions/gsd.cjs",
+  "gsd-core/VERSION",
+  "gsd-core/bin/check-latest-version.cjs",
+  "gsd-core/bin/ensure-runtime-build.cjs",
+  "gsd-core/bin/gsd-tools.cjs",
+  "gsd-core/bin/gsd_run",
+  "gsd-core/bin/shared/config-defaults.manifest.json",
+  "gsd-core/bin/shared/config-schema.manifest.json",
+  "gsd-core/bin/shared/model-catalog.json",
+  "gsd-core/bin/shared/runtime-aliases.manifest.json",
+  "gsd-core/bin/verify-reapply-patches.cjs",
+  "gsd-core/contexts/dev.md",
+  "gsd-core/contexts/research.md",
+  "gsd-core/contexts/review.md",
+  "gsd-core/references/agent-contracts.md",
+  "gsd-core/references/agent-skills-bootstrap.md",
+  "gsd-core/references/ai-evals.md",
+  "gsd-core/references/ai-frameworks.md",
+  "gsd-core/references/api-coverage.md",
+  "gsd-core/references/artifact-types.md",
+  "gsd-core/references/autonomous-smart-discuss.md",
+  "gsd-core/references/checkpoints.md",
+  "gsd-core/references/common-bug-patterns.md",
+  "gsd-core/references/context-budget.md",
+  "gsd-core/references/continuation-format.md",
+  "gsd-core/references/debugger-philosophy.md",
+  "gsd-core/references/decimal-phase-calculation.md",
+  "gsd-core/references/doc-conflict-engine.md",
+  "gsd-core/references/domain-probes.md",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/resolutions.json",
+  "gsd-core/references/edge-probe.md",
+  "gsd-core/references/execute-mvp-tdd.md",
+  "gsd-core/references/execute-phase-between-wave-reset.md",
+  "gsd-core/references/execute-phase-context-guard.md",
+  "gsd-core/references/execute-phase-wave-guard.md",
+  "gsd-core/references/executor-examples.md",
+  "gsd-core/references/few-shot-examples/plan-checker.md",
+  "gsd-core/references/few-shot-examples/verifier.md",
+  "gsd-core/references/gate-prompts.md",
+  "gsd-core/references/gates.md",
+  "gsd-core/references/git-integration.md",
+  "gsd-core/references/git-planning-commit.md",
+  "gsd-core/references/gsd-run-resolver.md",
+  "gsd-core/references/honest-verifier.md",
+  "gsd-core/references/ios-scaffold.md",
+  "gsd-core/references/loop-hook-dispatch.md",
+  "gsd-core/references/mandatory-initial-read.md",
+  "gsd-core/references/model-profile-resolution.md",
+  "gsd-core/references/model-profiles.md",
+  "gsd-core/references/mvp-concepts.md",
+  "gsd-core/references/phase-argument-parsing.md",
+  "gsd-core/references/planner-antipatterns.md",
+  "gsd-core/references/planner-chunked.md",
+  "gsd-core/references/planner-gap-closure.md",
+  "gsd-core/references/planner-graphify-auto-update.md",
+  "gsd-core/references/planner-guidance.md",
+  "gsd-core/references/planner-human-verify-mode.md",
+  "gsd-core/references/planner-interface-context.md",
+  "gsd-core/references/planner-load-graph-context.md",
+  "gsd-core/references/planner-mvp-mode.md",
+  "gsd-core/references/planner-reviews.md",
+  "gsd-core/references/planner-revision.md",
+  "gsd-core/references/planner-source-audit.md",
+  "gsd-core/references/planning-config.md",
+  "gsd-core/references/prohibition-probe-fixtures/01-streak-reminder/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/02-clean-utility/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/03-multi-prohibition/expected.json",
+  "gsd-core/references/prohibition-probe.md",
+  "gsd-core/references/project-skills-discovery.md",
+  "gsd-core/references/questioning.md",
+  "gsd-core/references/research-documentation-lookup.md",
+  "gsd-core/references/research-philosophy.md",
+  "gsd-core/references/research-verification-protocol.md",
+  "gsd-core/references/reviewer-instances.md",
+  "gsd-core/references/revision-loop.md",
+  "gsd-core/references/scout-codebase.md",
+  "gsd-core/references/security-asvs-levels.md",
+  "gsd-core/references/skeleton-template.md",
+  "gsd-core/references/sketch-interactivity.md",
+  "gsd-core/references/sketch-theme-system.md",
+  "gsd-core/references/sketch-tooling.md",
+  "gsd-core/references/sketch-variant-patterns.md",
+  "gsd-core/references/specless-probe-fallback.md",
+  "gsd-core/references/spidr-splitting.md",
+  "gsd-core/references/tdd.md",
+  "gsd-core/references/thinking-models-debug.md",
+  "gsd-core/references/thinking-models-execution.md",
+  "gsd-core/references/thinking-models-planning.md",
+  "gsd-core/references/thinking-models-research.md",
+  "gsd-core/references/thinking-models-verification.md",
+  "gsd-core/references/thinking-partner.md",
+  "gsd-core/references/ui-brand.md",
+  "gsd-core/references/ui-consideration-probe.md",
+  "gsd-core/references/universal-anti-patterns.md",
+  "gsd-core/references/untrusted-input-boundary.md",
+  "gsd-core/references/user-profiling.md",
+  "gsd-core/references/user-story-template.md",
+  "gsd-core/references/verification-overrides.md",
+  "gsd-core/references/verification-patterns.md",
+  "gsd-core/references/verify-mvp-mode.md",
+  "gsd-core/references/workstream-flag.md",
+  "gsd-core/references/worktree-branch-check.md",
+  "gsd-core/references/worktree-path-safety.md",
+  "gsd-core/templates/AI-SPEC.md",
+  "gsd-core/templates/DEBUG.md",
+  "gsd-core/templates/README.md",
+  "gsd-core/templates/SECURITY.md",
+  "gsd-core/templates/UAT.md",
+  "gsd-core/templates/UI-SPEC.md",
+  "gsd-core/templates/VALIDATION.md",
+  "gsd-core/templates/claude-md.md",
+  "gsd-core/templates/codebase/architecture.md",
+  "gsd-core/templates/codebase/concerns.md",
+  "gsd-core/templates/codebase/conventions.md",
+  "gsd-core/templates/codebase/integrations.md",
+  "gsd-core/templates/codebase/stack.md",
+  "gsd-core/templates/codebase/structure.md",
+  "gsd-core/templates/codebase/testing.md",
+  "gsd-core/templates/config.json",
+  "gsd-core/templates/context.md",
+  "gsd-core/templates/continue-here.md",
+  "gsd-core/templates/copilot-instructions.md",
+  "gsd-core/templates/debug-subagent-prompt.md",
+  "gsd-core/templates/dev-preferences.md",
+  "gsd-core/templates/discovery.md",
+  "gsd-core/templates/discussion-log.md",
+  "gsd-core/templates/milestone-archive.md",
+  "gsd-core/templates/milestone.md",
+  "gsd-core/templates/phase-prompt.md",
+  "gsd-core/templates/planner-subagent-prompt.md",
+  "gsd-core/templates/project.md",
+  "gsd-core/templates/requirements.md",
+  "gsd-core/templates/research-project/ARCHITECTURE.md",
+  "gsd-core/templates/research-project/FEATURES.md",
+  "gsd-core/templates/research-project/PITFALLS.md",
+  "gsd-core/templates/research-project/STACK.md",
+  "gsd-core/templates/research-project/SUMMARY.md",
+  "gsd-core/templates/research.md",
+  "gsd-core/templates/retrospective.md",
+  "gsd-core/templates/roadmap.md",
+  "gsd-core/templates/spec.md",
+  "gsd-core/templates/state.md",
+  "gsd-core/templates/summary-complex.md",
+  "gsd-core/templates/summary-minimal.md",
+  "gsd-core/templates/summary-standard.md",
+  "gsd-core/templates/summary.md",
+  "gsd-core/templates/user-profile.md",
+  "gsd-core/templates/user-setup.md",
+  "gsd-core/templates/verification-report.md",
+  "gsd-core/workflows/_runtime-launcher.snippet.sh",
+  "gsd-core/workflows/add-backlog.md",
+  "gsd-core/workflows/add-phase.md",
+  "gsd-core/workflows/add-tests.md",
+  "gsd-core/workflows/add-todo.md",
+  "gsd-core/workflows/ai-integration-phase.md",
+  "gsd-core/workflows/analyze-dependencies.md",
+  "gsd-core/workflows/audit-fix.md",
+  "gsd-core/workflows/audit-milestone.md",
+  "gsd-core/workflows/audit-uat.md",
+  "gsd-core/workflows/autonomous.md",
+  "gsd-core/workflows/check-todos.md",
+  "gsd-core/workflows/cleanup.md",
+  "gsd-core/workflows/code-review-fix.md",
+  "gsd-core/workflows/code-review.md",
+  "gsd-core/workflows/complete-milestone.md",
+  "gsd-core/workflows/debug.md",
+  "gsd-core/workflows/diagnose-issues.md",
+  "gsd-core/workflows/discovery-phase.md",
+  "gsd-core/workflows/discuss-phase-assumptions.md",
+  "gsd-core/workflows/discuss-phase-power.md",
+  "gsd-core/workflows/discuss-phase.md",
+  "gsd-core/workflows/discuss-phase/modes/advisor.md",
+  "gsd-core/workflows/discuss-phase/modes/all.md",
+  "gsd-core/workflows/discuss-phase/modes/analyze.md",
+  "gsd-core/workflows/discuss-phase/modes/auto.md",
+  "gsd-core/workflows/discuss-phase/modes/batch.md",
+  "gsd-core/workflows/discuss-phase/modes/chain.md",
+  "gsd-core/workflows/discuss-phase/modes/default.md",
+  "gsd-core/workflows/discuss-phase/modes/power.md",
+  "gsd-core/workflows/discuss-phase/modes/text.md",
+  "gsd-core/workflows/discuss-phase/templates/checkpoint.json",
+  "gsd-core/workflows/discuss-phase/templates/context.md",
+  "gsd-core/workflows/discuss-phase/templates/discussion-log.md",
+  "gsd-core/workflows/do.md",
+  "gsd-core/workflows/docs-update.md",
+  "gsd-core/workflows/edit-phase.md",
+  "gsd-core/workflows/eval-review.md",
+  "gsd-core/workflows/execute-phase.md",
+  "gsd-core/workflows/execute-phase/steps/codebase-drift-gate.md",
+  "gsd-core/workflows/execute-phase/steps/per-plan-worktree-gate.md",
+  "gsd-core/workflows/execute-phase/steps/post-merge-gate.md",
+  "gsd-core/workflows/execute-phase/steps/regression-gate.md",
+  "gsd-core/workflows/execute-phase/steps/worktree-recovery-policy.md",
+  "gsd-core/workflows/execute-plan.md",
+  "gsd-core/workflows/explore.md",
+  "gsd-core/workflows/extract-learnings.md",
+  "gsd-core/workflows/fast.md",
+  "gsd-core/workflows/forensics.md",
+  "gsd-core/workflows/graduation.md",
+  "gsd-core/workflows/health.md",
+  "gsd-core/workflows/help.md",
+  "gsd-core/workflows/help/modes/brief.md",
+  "gsd-core/workflows/help/modes/default.md",
+  "gsd-core/workflows/help/modes/full.md",
+  "gsd-core/workflows/help/modes/topic.md",
+  "gsd-core/workflows/import.md",
+  "gsd-core/workflows/inbox.md",
+  "gsd-core/workflows/ingest-docs.md",
+  "gsd-core/workflows/insert-phase.md",
+  "gsd-core/workflows/list-phase-assumptions.md",
+  "gsd-core/workflows/list-seeds.md",
+  "gsd-core/workflows/list-workspaces.md",
+  "gsd-core/workflows/manager.md",
+  "gsd-core/workflows/map-codebase.md",
+  "gsd-core/workflows/milestone-summary.md",
+  "gsd-core/workflows/mvp-phase.md",
+  "gsd-core/workflows/new-milestone.md",
+  "gsd-core/workflows/new-project.md",
+  "gsd-core/workflows/new-workspace.md",
+  "gsd-core/workflows/next.md",
+  "gsd-core/workflows/node-repair.md",
+  "gsd-core/workflows/note.md",
+  "gsd-core/workflows/onboard.md",
+  "gsd-core/workflows/pause-work.md",
+  "gsd-core/workflows/plan-milestone-gaps.md",
+  "gsd-core/workflows/plan-phase.md",
+  "gsd-core/workflows/plan-phase/steps/closed-phase-gate.md",
+  "gsd-core/workflows/plan-phase/steps/prd-express-path.md",
+  "gsd-core/workflows/plan-phase/steps/windows-troubleshooting.md",
+  "gsd-core/workflows/plan-review-convergence.md",
+  "gsd-core/workflows/plant-seed.md",
+  "gsd-core/workflows/pr-branch.md",
+  "gsd-core/workflows/profile-user.md",
+  "gsd-core/workflows/progress.md",
+  "gsd-core/workflows/quick.md",
+  "gsd-core/workflows/reapply-patches.md",
+  "gsd-core/workflows/remove-phase.md",
+  "gsd-core/workflows/remove-workspace.md",
+  "gsd-core/workflows/resume-project.md",
+  "gsd-core/workflows/review.md",
+  "gsd-core/workflows/scan.md",
+  "gsd-core/workflows/secure-phase.md",
+  "gsd-core/workflows/session-report.md",
+  "gsd-core/workflows/settings-advanced.md",
+  "gsd-core/workflows/settings-integrations.md",
+  "gsd-core/workflows/settings.md",
+  "gsd-core/workflows/ship.md",
+  "gsd-core/workflows/sketch-wrap-up.md",
+  "gsd-core/workflows/sketch.md",
+  "gsd-core/workflows/smart-entry.md",
+  "gsd-core/workflows/spec-phase.md",
+  "gsd-core/workflows/spike-wrap-up.md",
+  "gsd-core/workflows/spike.md",
+  "gsd-core/workflows/stats.md",
+  "gsd-core/workflows/sync-skills.md",
+  "gsd-core/workflows/thread.md",
+  "gsd-core/workflows/transition.md",
+  "gsd-core/workflows/ui-phase.md",
+  "gsd-core/workflows/ui-review.md",
+  "gsd-core/workflows/ultraplan-phase.md",
+  "gsd-core/workflows/undo.md",
+  "gsd-core/workflows/update.md",
+  "gsd-core/workflows/validate-phase.md",
+  "gsd-core/workflows/verify-phase.md",
+  "gsd-core/workflows/verify-work.md",
+  "hooks/gsd-check-update-worker.js",
+  "hooks/gsd-check-update.js",
+  "hooks/gsd-config-reload.js",
+  "hooks/gsd-context-monitor.js",
+  "hooks/gsd-cursor-post-tool.js",
+  "hooks/gsd-cursor-pre-tool.js",
+  "hooks/gsd-cursor-session-start.js",
+  "hooks/gsd-cursor-stop.js",
+  "hooks/gsd-cursor-subagent-start.js",
+  "hooks/gsd-cursor-subagent-stop.js",
+  "hooks/gsd-ensure-canonical-path.js",
+  "hooks/gsd-graphify-update.sh",
+  "hooks/gsd-phase-boundary.sh",
+  "hooks/gsd-prompt-guard.js",
+  "hooks/gsd-read-guard.js",
+  "hooks/gsd-read-injection-scanner.js",
+  "hooks/gsd-session-state.sh",
+  "hooks/gsd-statusline.js",
+  "hooks/gsd-update-banner.js",
+  "hooks/gsd-validate-commit.sh",
+  "hooks/gsd-windsurf-pre-command.js",
+  "hooks/gsd-windsurf-pre-write.js",
+  "hooks/gsd-workflow-guard.js",
+  "hooks/gsd-worktree-path-guard.js",
+  "hooks/lib/git-cmd.js",
+  "hooks/lib/gsd-graphify-rebuild.sh",
+  "hooks/managed-hooks-registry.cjs",
+  "package.json",
+  "scripts/changeset/README.md",
+  "scripts/changeset/cli.cjs",
+  "scripts/changeset/github-release-notes.cjs",
+  "scripts/changeset/lint.cjs",
+  "scripts/changeset/new.cjs",
+  "scripts/changeset/parse.cjs",
+  "scripts/changeset/render.cjs",
+  "scripts/changeset/serialize.cjs",
+  "scripts/fix-slash-commands.cjs",
+  "scripts/gen-capability-registry.cjs",
+  "scripts/gen-loop-host-contract.cjs",
+  "scripts/lib/allowlist-ratchet.cjs",
+  "scripts/lib/cli-exit.cjs"
+]
diff --git a/tests/fixtures/install-tree/qwen.json b/tests/fixtures/install-tree/qwen.json
new file mode 100644
index 000000000..d1d1e8dc9
--- /dev/null
+++ b/tests/fixtures/install-tree/qwen.json
@@ -0,0 +1,427 @@
+[
+  ".gsd-profile",
+  ".gsd/defaults.json",
+  "agents/gsd-advisor-researcher.md",
+  "agents/gsd-ai-researcher.md",
+  "agents/gsd-assumptions-analyzer.md",
+  "agents/gsd-code-fixer.md",
+  "agents/gsd-code-reviewer.md",
+  "agents/gsd-codebase-mapper.md",
+  "agents/gsd-debug-session-manager.md",
+  "agents/gsd-debugger.md",
+  "agents/gsd-doc-classifier.md",
+  "agents/gsd-doc-synthesizer.md",
+  "agents/gsd-doc-verifier.md",
+  "agents/gsd-doc-writer.md",
+  "agents/gsd-domain-researcher.md",
+  "agents/gsd-eval-auditor.md",
+  "agents/gsd-eval-planner.md",
+  "agents/gsd-executor.md",
+  "agents/gsd-framework-selector.md",
+  "agents/gsd-integration-checker.md",
+  "agents/gsd-intel-updater.md",
+  "agents/gsd-mempalace-curator.md",
+  "agents/gsd-nyquist-auditor.md",
+  "agents/gsd-pattern-mapper.md",
+  "agents/gsd-phase-researcher.md",
+  "agents/gsd-plan-checker.md",
+  "agents/gsd-planner.md",
+  "agents/gsd-project-researcher.md",
+  "agents/gsd-research-synthesizer.md",
+  "agents/gsd-roadmapper.md",
+  "agents/gsd-security-auditor.md",
+  "agents/gsd-ui-auditor.md",
+  "agents/gsd-ui-checker.md",
+  "agents/gsd-ui-researcher.md",
+  "agents/gsd-user-profiler.md",
+  "agents/gsd-verifier.md",
+  "gsd-core/VERSION",
+  "gsd-core/bin/check-latest-version.cjs",
+  "gsd-core/bin/ensure-runtime-build.cjs",
+  "gsd-core/bin/gsd-tools.cjs",
+  "gsd-core/bin/gsd_run",
+  "gsd-core/bin/shared/config-defaults.manifest.json",
+  "gsd-core/bin/shared/config-schema.manifest.json",
+  "gsd-core/bin/shared/model-catalog.json",
+  "gsd-core/bin/shared/runtime-aliases.manifest.json",
+  "gsd-core/bin/verify-reapply-patches.cjs",
+  "gsd-core/contexts/dev.md",
+  "gsd-core/contexts/research.md",
+  "gsd-core/contexts/review.md",
+  "gsd-core/references/agent-contracts.md",
+  "gsd-core/references/agent-skills-bootstrap.md",
+  "gsd-core/references/ai-evals.md",
+  "gsd-core/references/ai-frameworks.md",
+  "gsd-core/references/api-coverage.md",
+  "gsd-core/references/artifact-types.md",
+  "gsd-core/references/autonomous-smart-discuss.md",
+  "gsd-core/references/checkpoints.md",
+  "gsd-core/references/common-bug-patterns.md",
+  "gsd-core/references/context-budget.md",
+  "gsd-core/references/continuation-format.md",
+  "gsd-core/references/debugger-philosophy.md",
+  "gsd-core/references/decimal-phase-calculation.md",
+  "gsd-core/references/doc-conflict-engine.md",
+  "gsd-core/references/domain-probes.md",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/resolutions.json",
+  "gsd-core/references/edge-probe.md",
+  "gsd-core/references/execute-mvp-tdd.md",
+  "gsd-core/references/execute-phase-between-wave-reset.md",
+  "gsd-core/references/execute-phase-context-guard.md",
+  "gsd-core/references/execute-phase-wave-guard.md",
+  "gsd-core/references/executor-examples.md",
+  "gsd-core/references/few-shot-examples/plan-checker.md",
+  "gsd-core/references/few-shot-examples/verifier.md",
+  "gsd-core/references/gate-prompts.md",
+  "gsd-core/references/gates.md",
+  "gsd-core/references/git-integration.md",
+  "gsd-core/references/git-planning-commit.md",
+  "gsd-core/references/gsd-run-resolver.md",
+  "gsd-core/references/honest-verifier.md",
+  "gsd-core/references/ios-scaffold.md",
+  "gsd-core/references/loop-hook-dispatch.md",
+  "gsd-core/references/mandatory-initial-read.md",
+  "gsd-core/references/model-profile-resolution.md",
+  "gsd-core/references/model-profiles.md",
+  "gsd-core/references/mvp-concepts.md",
+  "gsd-core/references/phase-argument-parsing.md",
+  "gsd-core/references/planner-antipatterns.md",
+  "gsd-core/references/planner-chunked.md",
+  "gsd-core/references/planner-gap-closure.md",
+  "gsd-core/references/planner-graphify-auto-update.md",
+  "gsd-core/references/planner-guidance.md",
+  "gsd-core/references/planner-human-verify-mode.md",
+  "gsd-core/references/planner-interface-context.md",
+  "gsd-core/references/planner-load-graph-context.md",
+  "gsd-core/references/planner-mvp-mode.md",
+  "gsd-core/references/planner-reviews.md",
+  "gsd-core/references/planner-revision.md",
+  "gsd-core/references/planner-source-audit.md",
+  "gsd-core/references/planning-config.md",
+  "gsd-core/references/prohibition-probe-fixtures/01-streak-reminder/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/02-clean-utility/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/03-multi-prohibition/expected.json",
+  "gsd-core/references/prohibition-probe.md",
+  "gsd-core/references/project-skills-discovery.md",
+  "gsd-core/references/questioning.md",
+  "gsd-core/references/research-documentation-lookup.md",
+  "gsd-core/references/research-philosophy.md",
+  "gsd-core/references/research-verification-protocol.md",
+  "gsd-core/references/reviewer-instances.md",
+  "gsd-core/references/revision-loop.md",
+  "gsd-core/references/scout-codebase.md",
+  "gsd-core/references/security-asvs-levels.md",
+  "gsd-core/references/skeleton-template.md",
+  "gsd-core/references/sketch-interactivity.md",
+  "gsd-core/references/sketch-theme-system.md",
+  "gsd-core/references/sketch-tooling.md",
+  "gsd-core/references/sketch-variant-patterns.md",
+  "gsd-core/references/specless-probe-fallback.md",
+  "gsd-core/references/spidr-splitting.md",
+  "gsd-core/references/tdd.md",
+  "gsd-core/references/thinking-models-debug.md",
+  "gsd-core/references/thinking-models-execution.md",
+  "gsd-core/references/thinking-models-planning.md",
+  "gsd-core/references/thinking-models-research.md",
+  "gsd-core/references/thinking-models-verification.md",
+  "gsd-core/references/thinking-partner.md",
+  "gsd-core/references/ui-brand.md",
+  "gsd-core/references/ui-consideration-probe.md",
+  "gsd-core/references/universal-anti-patterns.md",
+  "gsd-core/references/untrusted-input-boundary.md",
+  "gsd-core/references/user-profiling.md",
+  "gsd-core/references/user-story-template.md",
+  "gsd-core/references/verification-overrides.md",
+  "gsd-core/references/verification-patterns.md",
+  "gsd-core/references/verify-mvp-mode.md",
+  "gsd-core/references/workstream-flag.md",
+  "gsd-core/references/worktree-branch-check.md",
+  "gsd-core/references/worktree-path-safety.md",
+  "gsd-core/templates/AI-SPEC.md",
+  "gsd-core/templates/DEBUG.md",
+  "gsd-core/templates/README.md",
+  "gsd-core/templates/SECURITY.md",
+  "gsd-core/templates/UAT.md",
+  "gsd-core/templates/UI-SPEC.md",
+  "gsd-core/templates/VALIDATION.md",
+  "gsd-core/templates/claude-md.md",
+  "gsd-core/templates/codebase/architecture.md",
+  "gsd-core/templates/codebase/concerns.md",
+  "gsd-core/templates/codebase/conventions.md",
+  "gsd-core/templates/codebase/integrations.md",
+  "gsd-core/templates/codebase/stack.md",
+  "gsd-core/templates/codebase/structure.md",
+  "gsd-core/templates/codebase/testing.md",
+  "gsd-core/templates/config.json",
+  "gsd-core/templates/context.md",
+  "gsd-core/templates/continue-here.md",
+  "gsd-core/templates/copilot-instructions.md",
+  "gsd-core/templates/debug-subagent-prompt.md",
+  "gsd-core/templates/dev-preferences.md",
+  "gsd-core/templates/discovery.md",
+  "gsd-core/templates/discussion-log.md",
+  "gsd-core/templates/milestone-archive.md",
+  "gsd-core/templates/milestone.md",
+  "gsd-core/templates/phase-prompt.md",
+  "gsd-core/templates/planner-subagent-prompt.md",
+  "gsd-core/templates/project.md",
+  "gsd-core/templates/requirements.md",
+  "gsd-core/templates/research-project/ARCHITECTURE.md",
+  "gsd-core/templates/research-project/FEATURES.md",
+  "gsd-core/templates/research-project/PITFALLS.md",
+  "gsd-core/templates/research-project/STACK.md",
+  "gsd-core/templates/research-project/SUMMARY.md",
+  "gsd-core/templates/research.md",
+  "gsd-core/templates/retrospective.md",
+  "gsd-core/templates/roadmap.md",
+  "gsd-core/templates/spec.md",
+  "gsd-core/templates/state.md",
+  "gsd-core/templates/summary-complex.md",
+  "gsd-core/templates/summary-minimal.md",
+  "gsd-core/templates/summary-standard.md",
+  "gsd-core/templates/summary.md",
+  "gsd-core/templates/user-profile.md",
+  "gsd-core/templates/user-setup.md",
+  "gsd-core/templates/verification-report.md",
+  "gsd-core/workflows/_runtime-launcher.snippet.sh",
+  "gsd-core/workflows/add-backlog.md",
+  "gsd-core/workflows/add-phase.md",
+  "gsd-core/workflows/add-tests.md",
+  "gsd-core/workflows/add-todo.md",
+  "gsd-core/workflows/ai-integration-phase.md",
+  "gsd-core/workflows/analyze-dependencies.md",
+  "gsd-core/workflows/audit-fix.md",
+  "gsd-core/workflows/audit-milestone.md",
+  "gsd-core/workflows/audit-uat.md",
+  "gsd-core/workflows/autonomous.md",
+  "gsd-core/workflows/check-todos.md",
+  "gsd-core/workflows/cleanup.md",
+  "gsd-core/workflows/code-review-fix.md",
+  "gsd-core/workflows/code-review.md",
+  "gsd-core/workflows/complete-milestone.md",
+  "gsd-core/workflows/debug.md",
+  "gsd-core/workflows/diagnose-issues.md",
+  "gsd-core/workflows/discovery-phase.md",
+  "gsd-core/workflows/discuss-phase-assumptions.md",
+  "gsd-core/workflows/discuss-phase-power.md",
+  "gsd-core/workflows/discuss-phase.md",
+  "gsd-core/workflows/discuss-phase/modes/advisor.md",
+  "gsd-core/workflows/discuss-phase/modes/all.md",
+  "gsd-core/workflows/discuss-phase/modes/analyze.md",
+  "gsd-core/workflows/discuss-phase/modes/auto.md",
+  "gsd-core/workflows/discuss-phase/modes/batch.md",
+  "gsd-core/workflows/discuss-phase/modes/chain.md",
+  "gsd-core/workflows/discuss-phase/modes/default.md",
+  "gsd-core/workflows/discuss-phase/modes/power.md",
+  "gsd-core/workflows/discuss-phase/modes/text.md",
+  "gsd-core/workflows/discuss-phase/templates/checkpoint.json",
+  "gsd-core/workflows/discuss-phase/templates/context.md",
+  "gsd-core/workflows/discuss-phase/templates/discussion-log.md",
+  "gsd-core/workflows/do.md",
+  "gsd-core/workflows/docs-update.md",
+  "gsd-core/workflows/edit-phase.md",
+  "gsd-core/workflows/eval-review.md",
+  "gsd-core/workflows/execute-phase.md",
+  "gsd-core/workflows/execute-phase/steps/codebase-drift-gate.md",
+  "gsd-core/workflows/execute-phase/steps/per-plan-worktree-gate.md",
+  "gsd-core/workflows/execute-phase/steps/post-merge-gate.md",
+  "gsd-core/workflows/execute-phase/steps/regression-gate.md",
+  "gsd-core/workflows/execute-phase/steps/worktree-recovery-policy.md",
+  "gsd-core/workflows/execute-plan.md",
+  "gsd-core/workflows/explore.md",
+  "gsd-core/workflows/extract-learnings.md",
+  "gsd-core/workflows/fast.md",
+  "gsd-core/workflows/forensics.md",
+  "gsd-core/workflows/graduation.md",
+  "gsd-core/workflows/health.md",
+  "gsd-core/workflows/help.md",
+  "gsd-core/workflows/help/modes/brief.md",
+  "gsd-core/workflows/help/modes/default.md",
+  "gsd-core/workflows/help/modes/full.md",
+  "gsd-core/workflows/help/modes/topic.md",
+  "gsd-core/workflows/import.md",
+  "gsd-core/workflows/inbox.md",
+  "gsd-core/workflows/ingest-docs.md",
+  "gsd-core/workflows/insert-phase.md",
+  "gsd-core/workflows/list-phase-assumptions.md",
+  "gsd-core/workflows/list-seeds.md",
+  "gsd-core/workflows/list-workspaces.md",
+  "gsd-core/workflows/manager.md",
+  "gsd-core/workflows/map-codebase.md",
+  "gsd-core/workflows/milestone-summary.md",
+  "gsd-core/workflows/mvp-phase.md",
+  "gsd-core/workflows/new-milestone.md",
+  "gsd-core/workflows/new-project.md",
+  "gsd-core/workflows/new-workspace.md",
+  "gsd-core/workflows/next.md",
+  "gsd-core/workflows/node-repair.md",
+  "gsd-core/workflows/note.md",
+  "gsd-core/workflows/onboard.md",
+  "gsd-core/workflows/pause-work.md",
+  "gsd-core/workflows/plan-milestone-gaps.md",
+  "gsd-core/workflows/plan-phase.md",
+  "gsd-core/workflows/plan-phase/steps/closed-phase-gate.md",
+  "gsd-core/workflows/plan-phase/steps/prd-express-path.md",
+  "gsd-core/workflows/plan-phase/steps/windows-troubleshooting.md",
+  "gsd-core/workflows/plan-review-convergence.md",
+  "gsd-core/workflows/plant-seed.md",
+  "gsd-core/workflows/pr-branch.md",
+  "gsd-core/workflows/profile-user.md",
+  "gsd-core/workflows/progress.md",
+  "gsd-core/workflows/quick.md",
+  "gsd-core/workflows/reapply-patches.md",
+  "gsd-core/workflows/remove-phase.md",
+  "gsd-core/workflows/remove-workspace.md",
+  "gsd-core/workflows/resume-project.md",
+  "gsd-core/workflows/review.md",
+  "gsd-core/workflows/scan.md",
+  "gsd-core/workflows/secure-phase.md",
+  "gsd-core/workflows/session-report.md",
+  "gsd-core/workflows/settings-advanced.md",
+  "gsd-core/workflows/settings-integrations.md",
+  "gsd-core/workflows/settings.md",
+  "gsd-core/workflows/ship.md",
+  "gsd-core/workflows/sketch-wrap-up.md",
+  "gsd-core/workflows/sketch.md",
+  "gsd-core/workflows/smart-entry.md",
+  "gsd-core/workflows/spec-phase.md",
+  "gsd-core/workflows/spike-wrap-up.md",
+  "gsd-core/workflows/spike.md",
+  "gsd-core/workflows/stats.md",
+  "gsd-core/workflows/sync-skills.md",
+  "gsd-core/workflows/thread.md",
+  "gsd-core/workflows/transition.md",
+  "gsd-core/workflows/ui-phase.md",
+  "gsd-core/workflows/ui-review.md",
+  "gsd-core/workflows/ultraplan-phase.md",
+  "gsd-core/workflows/undo.md",
+  "gsd-core/workflows/update.md",
+  "gsd-core/workflows/validate-phase.md",
+  "gsd-core/workflows/verify-phase.md",
+  "gsd-core/workflows/verify-work.md",
+  "hooks/gsd-check-update-worker.js",
+  "hooks/gsd-check-update.js",
+  "hooks/gsd-config-reload.js",
+  "hooks/gsd-context-monitor.js",
+  "hooks/gsd-cursor-post-tool.js",
+  "hooks/gsd-cursor-pre-tool.js",
+  "hooks/gsd-cursor-session-start.js",
+  "hooks/gsd-cursor-stop.js",
+  "hooks/gsd-cursor-subagent-start.js",
+  "hooks/gsd-cursor-subagent-stop.js",
+  "hooks/gsd-ensure-canonical-path.js",
+  "hooks/gsd-graphify-update.sh",
+  "hooks/gsd-phase-boundary.sh",
+  "hooks/gsd-prompt-guard.js",
+  "hooks/gsd-read-guard.js",
+  "hooks/gsd-read-injection-scanner.js",
+  "hooks/gsd-session-state.sh",
+  "hooks/gsd-statusline.js",
+  "hooks/gsd-update-banner.js",
+  "hooks/gsd-validate-commit.sh",
+  "hooks/gsd-windsurf-pre-command.js",
+  "hooks/gsd-windsurf-pre-write.js",
+  "hooks/gsd-workflow-guard.js",
+  "hooks/gsd-worktree-path-guard.js",
+  "hooks/lib/git-cmd.js",
+  "hooks/lib/gsd-graphify-rebuild.sh",
+  "hooks/managed-hooks-registry.cjs",
+  "package.json",
+  "scripts/changeset/README.md",
+  "scripts/changeset/cli.cjs",
+  "scripts/changeset/github-release-notes.cjs",
+  "scripts/changeset/lint.cjs",
+  "scripts/changeset/new.cjs",
+  "scripts/changeset/parse.cjs",
+  "scripts/changeset/render.cjs",
+  "scripts/changeset/serialize.cjs",
+  "scripts/fix-slash-commands.cjs",
+  "scripts/gen-capability-registry.cjs",
+  "scripts/gen-loop-host-contract.cjs",
+  "scripts/lib/allowlist-ratchet.cjs",
+  "scripts/lib/cli-exit.cjs",
+  "skills/gsd-ns-context/SKILL.md",
+  "skills/gsd-ns-context/skills/docs-update/SKILL.md",
+  "skills/gsd-ns-context/skills/extract-learnings/SKILL.md",
+  "skills/gsd-ns-context/skills/graphify/SKILL.md",
+  "skills/gsd-ns-context/skills/map-codebase/SKILL.md",
+  "skills/gsd-ns-context/skills/mempalace-capture/SKILL.md",
+  "skills/gsd-ns-context/skills/mempalace-recall/SKILL.md",
+  "skills/gsd-ns-ideate/SKILL.md",
+  "skills/gsd-ns-ideate/skills/capture/SKILL.md",
+  "skills/gsd-ns-ideate/skills/explore/SKILL.md",
+  "skills/gsd-ns-ideate/skills/sketch/SKILL.md",
+  "skills/gsd-ns-ideate/skills/spec-phase/SKILL.md",
+  "skills/gsd-ns-ideate/skills/spike/SKILL.md",
+  "skills/gsd-ns-manage/SKILL.md",
+  "skills/gsd-ns-manage/skills/cleanup/SKILL.md",
+  "skills/gsd-ns-manage/skills/config/SKILL.md",
+  "skills/gsd-ns-manage/skills/health/SKILL.md",
+  "skills/gsd-ns-manage/skills/help/SKILL.md",
+  "skills/gsd-ns-manage/skills/inbox/SKILL.md",
+  "skills/gsd-ns-manage/skills/manager/SKILL.md",
+  "skills/gsd-ns-manage/skills/pause-work/SKILL.md",
+  "skills/gsd-ns-manage/skills/pr-branch/SKILL.md",
+  "skills/gsd-ns-manage/skills/resume-work/SKILL.md",
+  "skills/gsd-ns-manage/skills/settings/SKILL.md",
+  "skills/gsd-ns-manage/skills/ship/SKILL.md",
+  "skills/gsd-ns-manage/skills/stats/SKILL.md",
+  "skills/gsd-ns-manage/skills/surface/SKILL.md",
+  "skills/gsd-ns-manage/skills/thread/SKILL.md",
+  "skills/gsd-ns-manage/skills/undo/SKILL.md",
+  "skills/gsd-ns-manage/skills/update/SKILL.md",
+  "skills/gsd-ns-manage/skills/workspace/SKILL.md",
+  "skills/gsd-ns-manage/skills/workstreams/SKILL.md",
+  "skills/gsd-ns-project/SKILL.md",
+  "skills/gsd-ns-project/skills/audit-milestone/SKILL.md",
+  "skills/gsd-ns-project/skills/complete-milestone/SKILL.md",
+  "skills/gsd-ns-project/skills/import/SKILL.md",
+  "skills/gsd-ns-project/skills/ingest-docs/SKILL.md",
+  "skills/gsd-ns-project/skills/milestone-summary/SKILL.md",
+  "skills/gsd-ns-project/skills/new-milestone/SKILL.md",
+  "skills/gsd-ns-project/skills/new-project/SKILL.md",
+  "skills/gsd-ns-project/skills/onboard/SKILL.md",
+  "skills/gsd-ns-project/skills/profile-user/SKILL.md",
+  "skills/gsd-ns-project/skills/review-backlog/SKILL.md",
+  "skills/gsd-ns-review/SKILL.md",
+  "skills/gsd-ns-review/skills/audit-fix/SKILL.md",
+  "skills/gsd-ns-review/skills/audit-uat/SKILL.md",
+  "skills/gsd-ns-review/skills/code-review/SKILL.md",
+  "skills/gsd-ns-review/skills/debug/SKILL.md",
+  "skills/gsd-ns-review/skills/eval-review/SKILL.md",
+  "skills/gsd-ns-review/skills/forensics/SKILL.md",
+  "skills/gsd-ns-review/skills/review/SKILL.md",
+  "skills/gsd-ns-review/skills/secure-phase/SKILL.md",
+  "skills/gsd-ns-review/skills/ui-phase/SKILL.md",
+  "skills/gsd-ns-review/skills/ui-review/SKILL.md",
+  "skills/gsd-ns-review/skills/validate-phase/SKILL.md",
+  "skills/gsd-ns-workflow/SKILL.md",
+  "skills/gsd-ns-workflow/skills/add-tests/SKILL.md",
+  "skills/gsd-ns-workflow/skills/ai-integration-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/autonomous/SKILL.md",
+  "skills/gsd-ns-workflow/skills/discuss-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/execute-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/fast/SKILL.md",
+  "skills/gsd-ns-workflow/skills/mvp-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/next/SKILL.md",
+  "skills/gsd-ns-workflow/skills/phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/plan-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/plan-review-convergence/SKILL.md",
+  "skills/gsd-ns-workflow/skills/progress/SKILL.md",
+  "skills/gsd-ns-workflow/skills/quick/SKILL.md",
+  "skills/gsd-ns-workflow/skills/spec-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/ultraplan-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/verify-work/SKILL.md"
+]
diff --git a/tests/fixtures/install-tree/trae.json b/tests/fixtures/install-tree/trae.json
new file mode 100644
index 000000000..401b9fa55
--- /dev/null
+++ b/tests/fixtures/install-tree/trae.json
@@ -0,0 +1,399 @@
+[
+  ".gsd-profile",
+  ".gsd/defaults.json",
+  "agents/gsd-advisor-researcher.md",
+  "agents/gsd-ai-researcher.md",
+  "agents/gsd-assumptions-analyzer.md",
+  "agents/gsd-code-fixer.md",
+  "agents/gsd-code-reviewer.md",
+  "agents/gsd-codebase-mapper.md",
+  "agents/gsd-debug-session-manager.md",
+  "agents/gsd-debugger.md",
+  "agents/gsd-doc-classifier.md",
+  "agents/gsd-doc-synthesizer.md",
+  "agents/gsd-doc-verifier.md",
+  "agents/gsd-doc-writer.md",
+  "agents/gsd-domain-researcher.md",
+  "agents/gsd-eval-auditor.md",
+  "agents/gsd-eval-planner.md",
+  "agents/gsd-executor.md",
+  "agents/gsd-framework-selector.md",
+  "agents/gsd-integration-checker.md",
+  "agents/gsd-intel-updater.md",
+  "agents/gsd-mempalace-curator.md",
+  "agents/gsd-nyquist-auditor.md",
+  "agents/gsd-pattern-mapper.md",
+  "agents/gsd-phase-researcher.md",
+  "agents/gsd-plan-checker.md",
+  "agents/gsd-planner.md",
+  "agents/gsd-project-researcher.md",
+  "agents/gsd-research-synthesizer.md",
+  "agents/gsd-roadmapper.md",
+  "agents/gsd-security-auditor.md",
+  "agents/gsd-ui-auditor.md",
+  "agents/gsd-ui-checker.md",
+  "agents/gsd-ui-researcher.md",
+  "agents/gsd-user-profiler.md",
+  "agents/gsd-verifier.md",
+  "gsd-core/VERSION",
+  "gsd-core/bin/check-latest-version.cjs",
+  "gsd-core/bin/ensure-runtime-build.cjs",
+  "gsd-core/bin/gsd-tools.cjs",
+  "gsd-core/bin/gsd_run",
+  "gsd-core/bin/shared/config-defaults.manifest.json",
+  "gsd-core/bin/shared/config-schema.manifest.json",
+  "gsd-core/bin/shared/model-catalog.json",
+  "gsd-core/bin/shared/runtime-aliases.manifest.json",
+  "gsd-core/bin/verify-reapply-patches.cjs",
+  "gsd-core/contexts/dev.md",
+  "gsd-core/contexts/research.md",
+  "gsd-core/contexts/review.md",
+  "gsd-core/references/agent-contracts.md",
+  "gsd-core/references/agent-skills-bootstrap.md",
+  "gsd-core/references/ai-evals.md",
+  "gsd-core/references/ai-frameworks.md",
+  "gsd-core/references/api-coverage.md",
+  "gsd-core/references/artifact-types.md",
+  "gsd-core/references/autonomous-smart-discuss.md",
+  "gsd-core/references/checkpoints.md",
+  "gsd-core/references/common-bug-patterns.md",
+  "gsd-core/references/context-budget.md",
+  "gsd-core/references/continuation-format.md",
+  "gsd-core/references/debugger-philosophy.md",
+  "gsd-core/references/decimal-phase-calculation.md",
+  "gsd-core/references/doc-conflict-engine.md",
+  "gsd-core/references/domain-probes.md",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/resolutions.json",
+  "gsd-core/references/edge-probe.md",
+  "gsd-core/references/execute-mvp-tdd.md",
+  "gsd-core/references/execute-phase-between-wave-reset.md",
+  "gsd-core/references/execute-phase-context-guard.md",
+  "gsd-core/references/execute-phase-wave-guard.md",
+  "gsd-core/references/executor-examples.md",
+  "gsd-core/references/few-shot-examples/plan-checker.md",
+  "gsd-core/references/few-shot-examples/verifier.md",
+  "gsd-core/references/gate-prompts.md",
+  "gsd-core/references/gates.md",
+  "gsd-core/references/git-integration.md",
+  "gsd-core/references/git-planning-commit.md",
+  "gsd-core/references/gsd-run-resolver.md",
+  "gsd-core/references/honest-verifier.md",
+  "gsd-core/references/ios-scaffold.md",
+  "gsd-core/references/loop-hook-dispatch.md",
+  "gsd-core/references/mandatory-initial-read.md",
+  "gsd-core/references/model-profile-resolution.md",
+  "gsd-core/references/model-profiles.md",
+  "gsd-core/references/mvp-concepts.md",
+  "gsd-core/references/phase-argument-parsing.md",
+  "gsd-core/references/planner-antipatterns.md",
+  "gsd-core/references/planner-chunked.md",
+  "gsd-core/references/planner-gap-closure.md",
+  "gsd-core/references/planner-graphify-auto-update.md",
+  "gsd-core/references/planner-guidance.md",
+  "gsd-core/references/planner-human-verify-mode.md",
+  "gsd-core/references/planner-interface-context.md",
+  "gsd-core/references/planner-load-graph-context.md",
+  "gsd-core/references/planner-mvp-mode.md",
+  "gsd-core/references/planner-reviews.md",
+  "gsd-core/references/planner-revision.md",
+  "gsd-core/references/planner-source-audit.md",
+  "gsd-core/references/planning-config.md",
+  "gsd-core/references/prohibition-probe-fixtures/01-streak-reminder/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/02-clean-utility/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/03-multi-prohibition/expected.json",
+  "gsd-core/references/prohibition-probe.md",
+  "gsd-core/references/project-skills-discovery.md",
+  "gsd-core/references/questioning.md",
+  "gsd-core/references/research-documentation-lookup.md",
+  "gsd-core/references/research-philosophy.md",
+  "gsd-core/references/research-verification-protocol.md",
+  "gsd-core/references/reviewer-instances.md",
+  "gsd-core/references/revision-loop.md",
+  "gsd-core/references/scout-codebase.md",
+  "gsd-core/references/security-asvs-levels.md",
+  "gsd-core/references/skeleton-template.md",
+  "gsd-core/references/sketch-interactivity.md",
+  "gsd-core/references/sketch-theme-system.md",
+  "gsd-core/references/sketch-tooling.md",
+  "gsd-core/references/sketch-variant-patterns.md",
+  "gsd-core/references/specless-probe-fallback.md",
+  "gsd-core/references/spidr-splitting.md",
+  "gsd-core/references/tdd.md",
+  "gsd-core/references/thinking-models-debug.md",
+  "gsd-core/references/thinking-models-execution.md",
+  "gsd-core/references/thinking-models-planning.md",
+  "gsd-core/references/thinking-models-research.md",
+  "gsd-core/references/thinking-models-verification.md",
+  "gsd-core/references/thinking-partner.md",
+  "gsd-core/references/ui-brand.md",
+  "gsd-core/references/ui-consideration-probe.md",
+  "gsd-core/references/universal-anti-patterns.md",
+  "gsd-core/references/untrusted-input-boundary.md",
+  "gsd-core/references/user-profiling.md",
+  "gsd-core/references/user-story-template.md",
+  "gsd-core/references/verification-overrides.md",
+  "gsd-core/references/verification-patterns.md",
+  "gsd-core/references/verify-mvp-mode.md",
+  "gsd-core/references/workstream-flag.md",
+  "gsd-core/references/worktree-branch-check.md",
+  "gsd-core/references/worktree-path-safety.md",
+  "gsd-core/templates/AI-SPEC.md",
+  "gsd-core/templates/DEBUG.md",
+  "gsd-core/templates/README.md",
+  "gsd-core/templates/SECURITY.md",
+  "gsd-core/templates/UAT.md",
+  "gsd-core/templates/UI-SPEC.md",
+  "gsd-core/templates/VALIDATION.md",
+  "gsd-core/templates/claude-md.md",
+  "gsd-core/templates/codebase/architecture.md",
+  "gsd-core/templates/codebase/concerns.md",
+  "gsd-core/templates/codebase/conventions.md",
+  "gsd-core/templates/codebase/integrations.md",
+  "gsd-core/templates/codebase/stack.md",
+  "gsd-core/templates/codebase/structure.md",
+  "gsd-core/templates/codebase/testing.md",
+  "gsd-core/templates/config.json",
+  "gsd-core/templates/context.md",
+  "gsd-core/templates/continue-here.md",
+  "gsd-core/templates/copilot-instructions.md",
+  "gsd-core/templates/debug-subagent-prompt.md",
+  "gsd-core/templates/dev-preferences.md",
+  "gsd-core/templates/discovery.md",
+  "gsd-core/templates/discussion-log.md",
+  "gsd-core/templates/milestone-archive.md",
+  "gsd-core/templates/milestone.md",
+  "gsd-core/templates/phase-prompt.md",
+  "gsd-core/templates/planner-subagent-prompt.md",
+  "gsd-core/templates/project.md",
+  "gsd-core/templates/requirements.md",
+  "gsd-core/templates/research-project/ARCHITECTURE.md",
+  "gsd-core/templates/research-project/FEATURES.md",
+  "gsd-core/templates/research-project/PITFALLS.md",
+  "gsd-core/templates/research-project/STACK.md",
+  "gsd-core/templates/research-project/SUMMARY.md",
+  "gsd-core/templates/research.md",
+  "gsd-core/templates/retrospective.md",
+  "gsd-core/templates/roadmap.md",
+  "gsd-core/templates/spec.md",
+  "gsd-core/templates/state.md",
+  "gsd-core/templates/summary-complex.md",
+  "gsd-core/templates/summary-minimal.md",
+  "gsd-core/templates/summary-standard.md",
+  "gsd-core/templates/summary.md",
+  "gsd-core/templates/user-profile.md",
+  "gsd-core/templates/user-setup.md",
+  "gsd-core/templates/verification-report.md",
+  "gsd-core/workflows/_runtime-launcher.snippet.sh",
+  "gsd-core/workflows/add-backlog.md",
+  "gsd-core/workflows/add-phase.md",
+  "gsd-core/workflows/add-tests.md",
+  "gsd-core/workflows/add-todo.md",
+  "gsd-core/workflows/ai-integration-phase.md",
+  "gsd-core/workflows/analyze-dependencies.md",
+  "gsd-core/workflows/audit-fix.md",
+  "gsd-core/workflows/audit-milestone.md",
+  "gsd-core/workflows/audit-uat.md",
+  "gsd-core/workflows/autonomous.md",
+  "gsd-core/workflows/check-todos.md",
+  "gsd-core/workflows/cleanup.md",
+  "gsd-core/workflows/code-review-fix.md",
+  "gsd-core/workflows/code-review.md",
+  "gsd-core/workflows/complete-milestone.md",
+  "gsd-core/workflows/debug.md",
+  "gsd-core/workflows/diagnose-issues.md",
+  "gsd-core/workflows/discovery-phase.md",
+  "gsd-core/workflows/discuss-phase-assumptions.md",
+  "gsd-core/workflows/discuss-phase-power.md",
+  "gsd-core/workflows/discuss-phase.md",
+  "gsd-core/workflows/discuss-phase/modes/advisor.md",
+  "gsd-core/workflows/discuss-phase/modes/all.md",
+  "gsd-core/workflows/discuss-phase/modes/analyze.md",
+  "gsd-core/workflows/discuss-phase/modes/auto.md",
+  "gsd-core/workflows/discuss-phase/modes/batch.md",
+  "gsd-core/workflows/discuss-phase/modes/chain.md",
+  "gsd-core/workflows/discuss-phase/modes/default.md",
+  "gsd-core/workflows/discuss-phase/modes/power.md",
+  "gsd-core/workflows/discuss-phase/modes/text.md",
+  "gsd-core/workflows/discuss-phase/templates/checkpoint.json",
+  "gsd-core/workflows/discuss-phase/templates/context.md",
+  "gsd-core/workflows/discuss-phase/templates/discussion-log.md",
+  "gsd-core/workflows/do.md",
+  "gsd-core/workflows/docs-update.md",
+  "gsd-core/workflows/edit-phase.md",
+  "gsd-core/workflows/eval-review.md",
+  "gsd-core/workflows/execute-phase.md",
+  "gsd-core/workflows/execute-phase/steps/codebase-drift-gate.md",
+  "gsd-core/workflows/execute-phase/steps/per-plan-worktree-gate.md",
+  "gsd-core/workflows/execute-phase/steps/post-merge-gate.md",
+  "gsd-core/workflows/execute-phase/steps/regression-gate.md",
+  "gsd-core/workflows/execute-phase/steps/worktree-recovery-policy.md",
+  "gsd-core/workflows/execute-plan.md",
+  "gsd-core/workflows/explore.md",
+  "gsd-core/workflows/extract-learnings.md",
+  "gsd-core/workflows/fast.md",
+  "gsd-core/workflows/forensics.md",
+  "gsd-core/workflows/graduation.md",
+  "gsd-core/workflows/health.md",
+  "gsd-core/workflows/help.md",
+  "gsd-core/workflows/help/modes/brief.md",
+  "gsd-core/workflows/help/modes/default.md",
+  "gsd-core/workflows/help/modes/full.md",
+  "gsd-core/workflows/help/modes/topic.md",
+  "gsd-core/workflows/import.md",
+  "gsd-core/workflows/inbox.md",
+  "gsd-core/workflows/ingest-docs.md",
+  "gsd-core/workflows/insert-phase.md",
+  "gsd-core/workflows/list-phase-assumptions.md",
+  "gsd-core/workflows/list-seeds.md",
+  "gsd-core/workflows/list-workspaces.md",
+  "gsd-core/workflows/manager.md",
+  "gsd-core/workflows/map-codebase.md",
+  "gsd-core/workflows/milestone-summary.md",
+  "gsd-core/workflows/mvp-phase.md",
+  "gsd-core/workflows/new-milestone.md",
+  "gsd-core/workflows/new-project.md",
+  "gsd-core/workflows/new-workspace.md",
+  "gsd-core/workflows/next.md",
+  "gsd-core/workflows/node-repair.md",
+  "gsd-core/workflows/note.md",
+  "gsd-core/workflows/onboard.md",
+  "gsd-core/workflows/pause-work.md",
+  "gsd-core/workflows/plan-milestone-gaps.md",
+  "gsd-core/workflows/plan-phase.md",
+  "gsd-core/workflows/plan-phase/steps/closed-phase-gate.md",
+  "gsd-core/workflows/plan-phase/steps/prd-express-path.md",
+  "gsd-core/workflows/plan-phase/steps/windows-troubleshooting.md",
+  "gsd-core/workflows/plan-review-convergence.md",
+  "gsd-core/workflows/plant-seed.md",
+  "gsd-core/workflows/pr-branch.md",
+  "gsd-core/workflows/profile-user.md",
+  "gsd-core/workflows/progress.md",
+  "gsd-core/workflows/quick.md",
+  "gsd-core/workflows/reapply-patches.md",
+  "gsd-core/workflows/remove-phase.md",
+  "gsd-core/workflows/remove-workspace.md",
+  "gsd-core/workflows/resume-project.md",
+  "gsd-core/workflows/review.md",
+  "gsd-core/workflows/scan.md",
+  "gsd-core/workflows/secure-phase.md",
+  "gsd-core/workflows/session-report.md",
+  "gsd-core/workflows/settings-advanced.md",
+  "gsd-core/workflows/settings-integrations.md",
+  "gsd-core/workflows/settings.md",
+  "gsd-core/workflows/ship.md",
+  "gsd-core/workflows/sketch-wrap-up.md",
+  "gsd-core/workflows/sketch.md",
+  "gsd-core/workflows/smart-entry.md",
+  "gsd-core/workflows/spec-phase.md",
+  "gsd-core/workflows/spike-wrap-up.md",
+  "gsd-core/workflows/spike.md",
+  "gsd-core/workflows/stats.md",
+  "gsd-core/workflows/sync-skills.md",
+  "gsd-core/workflows/thread.md",
+  "gsd-core/workflows/transition.md",
+  "gsd-core/workflows/ui-phase.md",
+  "gsd-core/workflows/ui-review.md",
+  "gsd-core/workflows/ultraplan-phase.md",
+  "gsd-core/workflows/undo.md",
+  "gsd-core/workflows/update.md",
+  "gsd-core/workflows/validate-phase.md",
+  "gsd-core/workflows/verify-phase.md",
+  "gsd-core/workflows/verify-work.md",
+  "scripts/changeset/README.md",
+  "scripts/changeset/cli.cjs",
+  "scripts/changeset/github-release-notes.cjs",
+  "scripts/changeset/lint.cjs",
+  "scripts/changeset/new.cjs",
+  "scripts/changeset/parse.cjs",
+  "scripts/changeset/render.cjs",
+  "scripts/changeset/serialize.cjs",
+  "scripts/fix-slash-commands.cjs",
+  "scripts/gen-capability-registry.cjs",
+  "scripts/gen-loop-host-contract.cjs",
+  "scripts/lib/allowlist-ratchet.cjs",
+  "scripts/lib/cli-exit.cjs",
+  "skills/gsd-ns-context/SKILL.md",
+  "skills/gsd-ns-context/skills/docs-update/SKILL.md",
+  "skills/gsd-ns-context/skills/extract-learnings/SKILL.md",
+  "skills/gsd-ns-context/skills/graphify/SKILL.md",
+  "skills/gsd-ns-context/skills/map-codebase/SKILL.md",
+  "skills/gsd-ns-context/skills/mempalace-capture/SKILL.md",
+  "skills/gsd-ns-context/skills/mempalace-recall/SKILL.md",
+  "skills/gsd-ns-ideate/SKILL.md",
+  "skills/gsd-ns-ideate/skills/capture/SKILL.md",
+  "skills/gsd-ns-ideate/skills/explore/SKILL.md",
+  "skills/gsd-ns-ideate/skills/sketch/SKILL.md",
+  "skills/gsd-ns-ideate/skills/spec-phase/SKILL.md",
+  "skills/gsd-ns-ideate/skills/spike/SKILL.md",
+  "skills/gsd-ns-manage/SKILL.md",
+  "skills/gsd-ns-manage/skills/cleanup/SKILL.md",
+  "skills/gsd-ns-manage/skills/config/SKILL.md",
+  "skills/gsd-ns-manage/skills/health/SKILL.md",
+  "skills/gsd-ns-manage/skills/help/SKILL.md",
+  "skills/gsd-ns-manage/skills/inbox/SKILL.md",
+  "skills/gsd-ns-manage/skills/manager/SKILL.md",
+  "skills/gsd-ns-manage/skills/pause-work/SKILL.md",
+  "skills/gsd-ns-manage/skills/pr-branch/SKILL.md",
+  "skills/gsd-ns-manage/skills/resume-work/SKILL.md",
+  "skills/gsd-ns-manage/skills/settings/SKILL.md",
+  "skills/gsd-ns-manage/skills/ship/SKILL.md",
+  "skills/gsd-ns-manage/skills/stats/SKILL.md",
+  "skills/gsd-ns-manage/skills/surface/SKILL.md",
+  "skills/gsd-ns-manage/skills/thread/SKILL.md",
+  "skills/gsd-ns-manage/skills/undo/SKILL.md",
+  "skills/gsd-ns-manage/skills/update/SKILL.md",
+  "skills/gsd-ns-manage/skills/workspace/SKILL.md",
+  "skills/gsd-ns-manage/skills/workstreams/SKILL.md",
+  "skills/gsd-ns-project/SKILL.md",
+  "skills/gsd-ns-project/skills/audit-milestone/SKILL.md",
+  "skills/gsd-ns-project/skills/complete-milestone/SKILL.md",
+  "skills/gsd-ns-project/skills/import/SKILL.md",
+  "skills/gsd-ns-project/skills/ingest-docs/SKILL.md",
+  "skills/gsd-ns-project/skills/milestone-summary/SKILL.md",
+  "skills/gsd-ns-project/skills/new-milestone/SKILL.md",
+  "skills/gsd-ns-project/skills/new-project/SKILL.md",
+  "skills/gsd-ns-project/skills/onboard/SKILL.md",
+  "skills/gsd-ns-project/skills/profile-user/SKILL.md",
+  "skills/gsd-ns-project/skills/review-backlog/SKILL.md",
+  "skills/gsd-ns-review/SKILL.md",
+  "skills/gsd-ns-review/skills/audit-fix/SKILL.md",
+  "skills/gsd-ns-review/skills/audit-uat/SKILL.md",
+  "skills/gsd-ns-review/skills/code-review/SKILL.md",
+  "skills/gsd-ns-review/skills/debug/SKILL.md",
+  "skills/gsd-ns-review/skills/eval-review/SKILL.md",
+  "skills/gsd-ns-review/skills/forensics/SKILL.md",
+  "skills/gsd-ns-review/skills/review/SKILL.md",
+  "skills/gsd-ns-review/skills/secure-phase/SKILL.md",
+  "skills/gsd-ns-review/skills/ui-phase/SKILL.md",
+  "skills/gsd-ns-review/skills/ui-review/SKILL.md",
+  "skills/gsd-ns-review/skills/validate-phase/SKILL.md",
+  "skills/gsd-ns-workflow/SKILL.md",
+  "skills/gsd-ns-workflow/skills/add-tests/SKILL.md",
+  "skills/gsd-ns-workflow/skills/ai-integration-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/autonomous/SKILL.md",
+  "skills/gsd-ns-workflow/skills/discuss-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/execute-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/fast/SKILL.md",
+  "skills/gsd-ns-workflow/skills/mvp-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/next/SKILL.md",
+  "skills/gsd-ns-workflow/skills/phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/plan-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/plan-review-convergence/SKILL.md",
+  "skills/gsd-ns-workflow/skills/progress/SKILL.md",
+  "skills/gsd-ns-workflow/skills/quick/SKILL.md",
+  "skills/gsd-ns-workflow/skills/spec-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/ultraplan-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/verify-work/SKILL.md"
+]
diff --git a/tests/fixtures/install-tree/windsurf.json b/tests/fixtures/install-tree/windsurf.json
new file mode 100644
index 000000000..eca97635e
--- /dev/null
+++ b/tests/fixtures/install-tree/windsurf.json
@@ -0,0 +1,329 @@
+[
+  ".gsd-profile",
+  ".gsd/defaults.json",
+  "agents/gsd-advisor-researcher.md",
+  "agents/gsd-ai-researcher.md",
+  "agents/gsd-assumptions-analyzer.md",
+  "agents/gsd-code-fixer.md",
+  "agents/gsd-code-reviewer.md",
+  "agents/gsd-codebase-mapper.md",
+  "agents/gsd-debug-session-manager.md",
+  "agents/gsd-debugger.md",
+  "agents/gsd-doc-classifier.md",
+  "agents/gsd-doc-synthesizer.md",
+  "agents/gsd-doc-verifier.md",
+  "agents/gsd-doc-writer.md",
+  "agents/gsd-domain-researcher.md",
+  "agents/gsd-eval-auditor.md",
+  "agents/gsd-eval-planner.md",
+  "agents/gsd-executor.md",
+  "agents/gsd-framework-selector.md",
+  "agents/gsd-integration-checker.md",
+  "agents/gsd-intel-updater.md",
+  "agents/gsd-mempalace-curator.md",
+  "agents/gsd-nyquist-auditor.md",
+  "agents/gsd-pattern-mapper.md",
+  "agents/gsd-phase-researcher.md",
+  "agents/gsd-plan-checker.md",
+  "agents/gsd-planner.md",
+  "agents/gsd-project-researcher.md",
+  "agents/gsd-research-synthesizer.md",
+  "agents/gsd-roadmapper.md",
+  "agents/gsd-security-auditor.md",
+  "agents/gsd-ui-auditor.md",
+  "agents/gsd-ui-checker.md",
+  "agents/gsd-ui-researcher.md",
+  "agents/gsd-user-profiler.md",
+  "agents/gsd-verifier.md",
+  "gsd-core/VERSION",
+  "gsd-core/bin/check-latest-version.cjs",
+  "gsd-core/bin/ensure-runtime-build.cjs",
+  "gsd-core/bin/gsd-tools.cjs",
+  "gsd-core/bin/gsd_run",
+  "gsd-core/bin/shared/config-defaults.manifest.json",
+  "gsd-core/bin/shared/config-schema.manifest.json",
+  "gsd-core/bin/shared/model-catalog.json",
+  "gsd-core/bin/shared/runtime-aliases.manifest.json",
+  "gsd-core/bin/verify-reapply-patches.cjs",
+  "gsd-core/contexts/dev.md",
+  "gsd-core/contexts/research.md",
+  "gsd-core/contexts/review.md",
+  "gsd-core/references/agent-contracts.md",
+  "gsd-core/references/agent-skills-bootstrap.md",
+  "gsd-core/references/ai-evals.md",
+  "gsd-core/references/ai-frameworks.md",
+  "gsd-core/references/api-coverage.md",
+  "gsd-core/references/artifact-types.md",
+  "gsd-core/references/autonomous-smart-discuss.md",
+  "gsd-core/references/checkpoints.md",
+  "gsd-core/references/common-bug-patterns.md",
+  "gsd-core/references/context-budget.md",
+  "gsd-core/references/continuation-format.md",
+  "gsd-core/references/debugger-philosophy.md",
+  "gsd-core/references/decimal-phase-calculation.md",
+  "gsd-core/references/doc-conflict-engine.md",
+  "gsd-core/references/domain-probes.md",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/resolutions.json",
+  "gsd-core/references/edge-probe.md",
+  "gsd-core/references/execute-mvp-tdd.md",
+  "gsd-core/references/execute-phase-between-wave-reset.md",
+  "gsd-core/references/execute-phase-context-guard.md",
+  "gsd-core/references/execute-phase-wave-guard.md",
+  "gsd-core/references/executor-examples.md",
+  "gsd-core/references/few-shot-examples/plan-checker.md",
+  "gsd-core/references/few-shot-examples/verifier.md",
+  "gsd-core/references/gate-prompts.md",
+  "gsd-core/references/gates.md",
+  "gsd-core/references/git-integration.md",
+  "gsd-core/references/git-planning-commit.md",
+  "gsd-core/references/gsd-run-resolver.md",
+  "gsd-core/references/honest-verifier.md",
+  "gsd-core/references/ios-scaffold.md",
+  "gsd-core/references/loop-hook-dispatch.md",
+  "gsd-core/references/mandatory-initial-read.md",
+  "gsd-core/references/model-profile-resolution.md",
+  "gsd-core/references/model-profiles.md",
+  "gsd-core/references/mvp-concepts.md",
+  "gsd-core/references/phase-argument-parsing.md",
+  "gsd-core/references/planner-antipatterns.md",
+  "gsd-core/references/planner-chunked.md",
+  "gsd-core/references/planner-gap-closure.md",
+  "gsd-core/references/planner-graphify-auto-update.md",
+  "gsd-core/references/planner-guidance.md",
+  "gsd-core/references/planner-human-verify-mode.md",
+  "gsd-core/references/planner-interface-context.md",
+  "gsd-core/references/planner-load-graph-context.md",
+  "gsd-core/references/planner-mvp-mode.md",
+  "gsd-core/references/planner-reviews.md",
+  "gsd-core/references/planner-revision.md",
+  "gsd-core/references/planner-source-audit.md",
+  "gsd-core/references/planning-config.md",
+  "gsd-core/references/prohibition-probe-fixtures/01-streak-reminder/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/02-clean-utility/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/03-multi-prohibition/expected.json",
+  "gsd-core/references/prohibition-probe.md",
+  "gsd-core/references/project-skills-discovery.md",
+  "gsd-core/references/questioning.md",
+  "gsd-core/references/research-documentation-lookup.md",
+  "gsd-core/references/research-philosophy.md",
+  "gsd-core/references/research-verification-protocol.md",
+  "gsd-core/references/reviewer-instances.md",
+  "gsd-core/references/revision-loop.md",
+  "gsd-core/references/scout-codebase.md",
+  "gsd-core/references/security-asvs-levels.md",
+  "gsd-core/references/skeleton-template.md",
+  "gsd-core/references/sketch-interactivity.md",
+  "gsd-core/references/sketch-theme-system.md",
+  "gsd-core/references/sketch-tooling.md",
+  "gsd-core/references/sketch-variant-patterns.md",
+  "gsd-core/references/specless-probe-fallback.md",
+  "gsd-core/references/spidr-splitting.md",
+  "gsd-core/references/tdd.md",
+  "gsd-core/references/thinking-models-debug.md",
+  "gsd-core/references/thinking-models-execution.md",
+  "gsd-core/references/thinking-models-planning.md",
+  "gsd-core/references/thinking-models-research.md",
+  "gsd-core/references/thinking-models-verification.md",
+  "gsd-core/references/thinking-partner.md",
+  "gsd-core/references/ui-brand.md",
+  "gsd-core/references/ui-consideration-probe.md",
+  "gsd-core/references/universal-anti-patterns.md",
+  "gsd-core/references/untrusted-input-boundary.md",
+  "gsd-core/references/user-profiling.md",
+  "gsd-core/references/user-story-template.md",
+  "gsd-core/references/verification-overrides.md",
+  "gsd-core/references/verification-patterns.md",
+  "gsd-core/references/verify-mvp-mode.md",
+  "gsd-core/references/workstream-flag.md",
+  "gsd-core/references/worktree-branch-check.md",
+  "gsd-core/references/worktree-path-safety.md",
+  "gsd-core/templates/AI-SPEC.md",
+  "gsd-core/templates/DEBUG.md",
+  "gsd-core/templates/README.md",
+  "gsd-core/templates/SECURITY.md",
+  "gsd-core/templates/UAT.md",
+  "gsd-core/templates/UI-SPEC.md",
+  "gsd-core/templates/VALIDATION.md",
+  "gsd-core/templates/claude-md.md",
+  "gsd-core/templates/codebase/architecture.md",
+  "gsd-core/templates/codebase/concerns.md",
+  "gsd-core/templates/codebase/conventions.md",
+  "gsd-core/templates/codebase/integrations.md",
+  "gsd-core/templates/codebase/stack.md",
+  "gsd-core/templates/codebase/structure.md",
+  "gsd-core/templates/codebase/testing.md",
+  "gsd-core/templates/config.json",
+  "gsd-core/templates/context.md",
+  "gsd-core/templates/continue-here.md",
+  "gsd-core/templates/copilot-instructions.md",
+  "gsd-core/templates/debug-subagent-prompt.md",
+  "gsd-core/templates/dev-preferences.md",
+  "gsd-core/templates/discovery.md",
+  "gsd-core/templates/discussion-log.md",
+  "gsd-core/templates/milestone-archive.md",
+  "gsd-core/templates/milestone.md",
+  "gsd-core/templates/phase-prompt.md",
+  "gsd-core/templates/planner-subagent-prompt.md",
+  "gsd-core/templates/project.md",
+  "gsd-core/templates/requirements.md",
+  "gsd-core/templates/research-project/ARCHITECTURE.md",
+  "gsd-core/templates/research-project/FEATURES.md",
+  "gsd-core/templates/research-project/PITFALLS.md",
+  "gsd-core/templates/research-project/STACK.md",
+  "gsd-core/templates/research-project/SUMMARY.md",
+  "gsd-core/templates/research.md",
+  "gsd-core/templates/retrospective.md",
+  "gsd-core/templates/roadmap.md",
+  "gsd-core/templates/spec.md",
+  "gsd-core/templates/state.md",
+  "gsd-core/templates/summary-complex.md",
+  "gsd-core/templates/summary-minimal.md",
+  "gsd-core/templates/summary-standard.md",
+  "gsd-core/templates/summary.md",
+  "gsd-core/templates/user-profile.md",
+  "gsd-core/templates/user-setup.md",
+  "gsd-core/templates/verification-report.md",
+  "gsd-core/workflows/_runtime-launcher.snippet.sh",
+  "gsd-core/workflows/add-backlog.md",
+  "gsd-core/workflows/add-phase.md",
+  "gsd-core/workflows/add-tests.md",
+  "gsd-core/workflows/add-todo.md",
+  "gsd-core/workflows/ai-integration-phase.md",
+  "gsd-core/workflows/analyze-dependencies.md",
+  "gsd-core/workflows/audit-fix.md",
+  "gsd-core/workflows/audit-milestone.md",
+  "gsd-core/workflows/audit-uat.md",
+  "gsd-core/workflows/autonomous.md",
+  "gsd-core/workflows/check-todos.md",
+  "gsd-core/workflows/cleanup.md",
+  "gsd-core/workflows/code-review-fix.md",
+  "gsd-core/workflows/code-review.md",
+  "gsd-core/workflows/complete-milestone.md",
+  "gsd-core/workflows/debug.md",
+  "gsd-core/workflows/diagnose-issues.md",
+  "gsd-core/workflows/discovery-phase.md",
+  "gsd-core/workflows/discuss-phase-assumptions.md",
+  "gsd-core/workflows/discuss-phase-power.md",
+  "gsd-core/workflows/discuss-phase.md",
+  "gsd-core/workflows/discuss-phase/modes/advisor.md",
+  "gsd-core/workflows/discuss-phase/modes/all.md",
+  "gsd-core/workflows/discuss-phase/modes/analyze.md",
+  "gsd-core/workflows/discuss-phase/modes/auto.md",
+  "gsd-core/workflows/discuss-phase/modes/batch.md",
+  "gsd-core/workflows/discuss-phase/modes/chain.md",
+  "gsd-core/workflows/discuss-phase/modes/default.md",
+  "gsd-core/workflows/discuss-phase/modes/power.md",
+  "gsd-core/workflows/discuss-phase/modes/text.md",
+  "gsd-core/workflows/discuss-phase/templates/checkpoint.json",
+  "gsd-core/workflows/discuss-phase/templates/context.md",
+  "gsd-core/workflows/discuss-phase/templates/discussion-log.md",
+  "gsd-core/workflows/do.md",
+  "gsd-core/workflows/docs-update.md",
+  "gsd-core/workflows/edit-phase.md",
+  "gsd-core/workflows/eval-review.md",
+  "gsd-core/workflows/execute-phase.md",
+  "gsd-core/workflows/execute-phase/steps/codebase-drift-gate.md",
+  "gsd-core/workflows/execute-phase/steps/per-plan-worktree-gate.md",
+  "gsd-core/workflows/execute-phase/steps/post-merge-gate.md",
+  "gsd-core/workflows/execute-phase/steps/regression-gate.md",
+  "gsd-core/workflows/execute-phase/steps/worktree-recovery-policy.md",
+  "gsd-core/workflows/execute-plan.md",
+  "gsd-core/workflows/explore.md",
+  "gsd-core/workflows/extract-learnings.md",
+  "gsd-core/workflows/fast.md",
+  "gsd-core/workflows/forensics.md",
+  "gsd-core/workflows/graduation.md",
+  "gsd-core/workflows/health.md",
+  "gsd-core/workflows/help.md",
+  "gsd-core/workflows/help/modes/brief.md",
+  "gsd-core/workflows/help/modes/default.md",
+  "gsd-core/workflows/help/modes/full.md",
+  "gsd-core/workflows/help/modes/topic.md",
+  "gsd-core/workflows/import.md",
+  "gsd-core/workflows/inbox.md",
+  "gsd-core/workflows/ingest-docs.md",
+  "gsd-core/workflows/insert-phase.md",
+  "gsd-core/workflows/list-phase-assumptions.md",
+  "gsd-core/workflows/list-seeds.md",
+  "gsd-core/workflows/list-workspaces.md",
+  "gsd-core/workflows/manager.md",
+  "gsd-core/workflows/map-codebase.md",
+  "gsd-core/workflows/milestone-summary.md",
+  "gsd-core/workflows/mvp-phase.md",
+  "gsd-core/workflows/new-milestone.md",
+  "gsd-core/workflows/new-project.md",
+  "gsd-core/workflows/new-workspace.md",
+  "gsd-core/workflows/next.md",
+  "gsd-core/workflows/node-repair.md",
+  "gsd-core/workflows/note.md",
+  "gsd-core/workflows/onboard.md",
+  "gsd-core/workflows/pause-work.md",
+  "gsd-core/workflows/plan-milestone-gaps.md",
+  "gsd-core/workflows/plan-phase.md",
+  "gsd-core/workflows/plan-phase/steps/closed-phase-gate.md",
+  "gsd-core/workflows/plan-phase/steps/prd-express-path.md",
+  "gsd-core/workflows/plan-phase/steps/windows-troubleshooting.md",
+  "gsd-core/workflows/plan-review-convergence.md",
+  "gsd-core/workflows/plant-seed.md",
+  "gsd-core/workflows/pr-branch.md",
+  "gsd-core/workflows/profile-user.md",
+  "gsd-core/workflows/progress.md",
+  "gsd-core/workflows/quick.md",
+  "gsd-core/workflows/reapply-patches.md",
+  "gsd-core/workflows/remove-phase.md",
+  "gsd-core/workflows/remove-workspace.md",
+  "gsd-core/workflows/resume-project.md",
+  "gsd-core/workflows/review.md",
+  "gsd-core/workflows/scan.md",
+  "gsd-core/workflows/secure-phase.md",
+  "gsd-core/workflows/session-report.md",
+  "gsd-core/workflows/settings-advanced.md",
+  "gsd-core/workflows/settings-integrations.md",
+  "gsd-core/workflows/settings.md",
+  "gsd-core/workflows/ship.md",
+  "gsd-core/workflows/sketch-wrap-up.md",
+  "gsd-core/workflows/sketch.md",
+  "gsd-core/workflows/smart-entry.md",
+  "gsd-core/workflows/spec-phase.md",
+  "gsd-core/workflows/spike-wrap-up.md",
+  "gsd-core/workflows/spike.md",
+  "gsd-core/workflows/stats.md",
+  "gsd-core/workflows/sync-skills.md",
+  "gsd-core/workflows/thread.md",
+  "gsd-core/workflows/transition.md",
+  "gsd-core/workflows/ui-phase.md",
+  "gsd-core/workflows/ui-review.md",
+  "gsd-core/workflows/ultraplan-phase.md",
+  "gsd-core/workflows/undo.md",
+  "gsd-core/workflows/update.md",
+  "gsd-core/workflows/validate-phase.md",
+  "gsd-core/workflows/verify-phase.md",
+  "gsd-core/workflows/verify-work.md",
+  "hooks/gsd-windsurf-pre-command.js",
+  "hooks/gsd-windsurf-pre-write.js",
+  "scripts/changeset/README.md",
+  "scripts/changeset/cli.cjs",
+  "scripts/changeset/github-release-notes.cjs",
+  "scripts/changeset/lint.cjs",
+  "scripts/changeset/new.cjs",
+  "scripts/changeset/parse.cjs",
+  "scripts/changeset/render.cjs",
+  "scripts/changeset/serialize.cjs",
+  "scripts/fix-slash-commands.cjs",
+  "scripts/gen-capability-registry.cjs",
+  "scripts/gen-loop-host-contract.cjs",
+  "scripts/lib/allowlist-ratchet.cjs",
+  "scripts/lib/cli-exit.cjs"
+]
diff --git a/tests/fixtures/install-tree/zcode.json b/tests/fixtures/install-tree/zcode.json
new file mode 100644
index 000000000..fc10b6b55
--- /dev/null
+++ b/tests/fixtures/install-tree/zcode.json
@@ -0,0 +1,470 @@
+[
+  ".gsd-profile",
+  ".gsd/defaults.json",
+  "agents/gsd-advisor-researcher.md",
+  "agents/gsd-ai-researcher.md",
+  "agents/gsd-assumptions-analyzer.md",
+  "agents/gsd-code-fixer.md",
+  "agents/gsd-code-reviewer.md",
+  "agents/gsd-codebase-mapper.md",
+  "agents/gsd-debug-session-manager.md",
+  "agents/gsd-debugger.md",
+  "agents/gsd-doc-classifier.md",
+  "agents/gsd-doc-synthesizer.md",
+  "agents/gsd-doc-verifier.md",
+  "agents/gsd-doc-writer.md",
+  "agents/gsd-domain-researcher.md",
+  "agents/gsd-eval-auditor.md",
+  "agents/gsd-eval-planner.md",
+  "agents/gsd-executor.md",
+  "agents/gsd-framework-selector.md",
+  "agents/gsd-integration-checker.md",
+  "agents/gsd-intel-updater.md",
+  "agents/gsd-mempalace-curator.md",
+  "agents/gsd-nyquist-auditor.md",
+  "agents/gsd-pattern-mapper.md",
+  "agents/gsd-phase-researcher.md",
+  "agents/gsd-plan-checker.md",
+  "agents/gsd-planner.md",
+  "agents/gsd-project-researcher.md",
+  "agents/gsd-research-synthesizer.md",
+  "agents/gsd-roadmapper.md",
+  "agents/gsd-security-auditor.md",
+  "agents/gsd-ui-auditor.md",
+  "agents/gsd-ui-checker.md",
+  "agents/gsd-ui-researcher.md",
+  "agents/gsd-user-profiler.md",
+  "agents/gsd-verifier.md",
+  "commands/gsd-add-tests.md",
+  "commands/gsd-ai-integration-phase.md",
+  "commands/gsd-audit-fix.md",
+  "commands/gsd-audit-milestone.md",
+  "commands/gsd-audit-uat.md",
+  "commands/gsd-autonomous.md",
+  "commands/gsd-capture.md",
+  "commands/gsd-cleanup.md",
+  "commands/gsd-code-review.md",
+  "commands/gsd-complete-milestone.md",
+  "commands/gsd-config.md",
+  "commands/gsd-debug.md",
+  "commands/gsd-discuss-phase.md",
+  "commands/gsd-docs-update.md",
+  "commands/gsd-eval-review.md",
+  "commands/gsd-execute-phase.md",
+  "commands/gsd-explore.md",
+  "commands/gsd-extract-learnings.md",
+  "commands/gsd-fast.md",
+  "commands/gsd-forensics.md",
+  "commands/gsd-graphify.md",
+  "commands/gsd-health.md",
+  "commands/gsd-help.md",
+  "commands/gsd-import.md",
+  "commands/gsd-inbox.md",
+  "commands/gsd-ingest-docs.md",
+  "commands/gsd-manager.md",
+  "commands/gsd-map-codebase.md",
+  "commands/gsd-mempalace-capture.md",
+  "commands/gsd-mempalace-recall.md",
+  "commands/gsd-milestone-summary.md",
+  "commands/gsd-mvp-phase.md",
+  "commands/gsd-new-milestone.md",
+  "commands/gsd-new-project.md",
+  "commands/gsd-next.md",
+  "commands/gsd-ns-context.md",
+  "commands/gsd-ns-ideate.md",
+  "commands/gsd-ns-manage.md",
+  "commands/gsd-ns-project.md",
+  "commands/gsd-ns-review.md",
+  "commands/gsd-ns-workflow.md",
+  "commands/gsd-onboard.md",
+  "commands/gsd-pause-work.md",
+  "commands/gsd-phase.md",
+  "commands/gsd-plan-phase.md",
+  "commands/gsd-plan-review-convergence.md",
+  "commands/gsd-pr-branch.md",
+  "commands/gsd-profile-user.md",
+  "commands/gsd-progress.md",
+  "commands/gsd-quick.md",
+  "commands/gsd-resume-work.md",
+  "commands/gsd-review-backlog.md",
+  "commands/gsd-review.md",
+  "commands/gsd-secure-phase.md",
+  "commands/gsd-settings.md",
+  "commands/gsd-ship.md",
+  "commands/gsd-sketch.md",
+  "commands/gsd-spec-phase.md",
+  "commands/gsd-spike.md",
+  "commands/gsd-stats.md",
+  "commands/gsd-surface.md",
+  "commands/gsd-thread.md",
+  "commands/gsd-ui-phase.md",
+  "commands/gsd-ui-review.md",
+  "commands/gsd-ultraplan-phase.md",
+  "commands/gsd-undo.md",
+  "commands/gsd-update.md",
+  "commands/gsd-validate-phase.md",
+  "commands/gsd-verify-work.md",
+  "commands/gsd-workspace.md",
+  "commands/gsd-workstreams.md",
+  "gsd-core/VERSION",
+  "gsd-core/bin/check-latest-version.cjs",
+  "gsd-core/bin/ensure-runtime-build.cjs",
+  "gsd-core/bin/gsd-tools.cjs",
+  "gsd-core/bin/gsd_run",
+  "gsd-core/bin/shared/config-defaults.manifest.json",
+  "gsd-core/bin/shared/config-schema.manifest.json",
+  "gsd-core/bin/shared/model-catalog.json",
+  "gsd-core/bin/shared/runtime-aliases.manifest.json",
+  "gsd-core/bin/verify-reapply-patches.cjs",
+  "gsd-core/contexts/dev.md",
+  "gsd-core/contexts/research.md",
+  "gsd-core/contexts/review.md",
+  "gsd-core/references/agent-contracts.md",
+  "gsd-core/references/agent-skills-bootstrap.md",
+  "gsd-core/references/ai-evals.md",
+  "gsd-core/references/ai-frameworks.md",
+  "gsd-core/references/api-coverage.md",
+  "gsd-core/references/artifact-types.md",
+  "gsd-core/references/autonomous-smart-discuss.md",
+  "gsd-core/references/checkpoints.md",
+  "gsd-core/references/common-bug-patterns.md",
+  "gsd-core/references/context-budget.md",
+  "gsd-core/references/continuation-format.md",
+  "gsd-core/references/debugger-philosophy.md",
+  "gsd-core/references/decimal-phase-calculation.md",
+  "gsd-core/references/doc-conflict-engine.md",
+  "gsd-core/references/domain-probes.md",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/01-round-half-even/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/02-merge-intervals/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/03-truncate-graphemes/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/04-money-rounding/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/05-list-dedupe/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/expected-coverage.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/requirements.json",
+  "gsd-core/references/edge-probe-fixtures/06-resolved-mixed/resolutions.json",
+  "gsd-core/references/edge-probe.md",
+  "gsd-core/references/execute-mvp-tdd.md",
+  "gsd-core/references/execute-phase-between-wave-reset.md",
+  "gsd-core/references/execute-phase-context-guard.md",
+  "gsd-core/references/execute-phase-wave-guard.md",
+  "gsd-core/references/executor-examples.md",
+  "gsd-core/references/few-shot-examples/plan-checker.md",
+  "gsd-core/references/few-shot-examples/verifier.md",
+  "gsd-core/references/gate-prompts.md",
+  "gsd-core/references/gates.md",
+  "gsd-core/references/git-integration.md",
+  "gsd-core/references/git-planning-commit.md",
+  "gsd-core/references/gsd-run-resolver.md",
+  "gsd-core/references/honest-verifier.md",
+  "gsd-core/references/ios-scaffold.md",
+  "gsd-core/references/loop-hook-dispatch.md",
+  "gsd-core/references/mandatory-initial-read.md",
+  "gsd-core/references/model-profile-resolution.md",
+  "gsd-core/references/model-profiles.md",
+  "gsd-core/references/mvp-concepts.md",
+  "gsd-core/references/phase-argument-parsing.md",
+  "gsd-core/references/planner-antipatterns.md",
+  "gsd-core/references/planner-chunked.md",
+  "gsd-core/references/planner-gap-closure.md",
+  "gsd-core/references/planner-graphify-auto-update.md",
+  "gsd-core/references/planner-guidance.md",
+  "gsd-core/references/planner-human-verify-mode.md",
+  "gsd-core/references/planner-interface-context.md",
+  "gsd-core/references/planner-load-graph-context.md",
+  "gsd-core/references/planner-mvp-mode.md",
+  "gsd-core/references/planner-reviews.md",
+  "gsd-core/references/planner-revision.md",
+  "gsd-core/references/planner-source-audit.md",
+  "gsd-core/references/planning-config.md",
+  "gsd-core/references/prohibition-probe-fixtures/01-streak-reminder/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/02-clean-utility/expected.json",
+  "gsd-core/references/prohibition-probe-fixtures/03-multi-prohibition/expected.json",
+  "gsd-core/references/prohibition-probe.md",
+  "gsd-core/references/project-skills-discovery.md",
+  "gsd-core/references/questioning.md",
+  "gsd-core/references/research-documentation-lookup.md",
+  "gsd-core/references/research-philosophy.md",
+  "gsd-core/references/research-verification-protocol.md",
+  "gsd-core/references/reviewer-instances.md",
+  "gsd-core/references/revision-loop.md",
+  "gsd-core/references/scout-codebase.md",
+  "gsd-core/references/security-asvs-levels.md",
+  "gsd-core/references/skeleton-template.md",
+  "gsd-core/references/sketch-interactivity.md",
+  "gsd-core/references/sketch-theme-system.md",
+  "gsd-core/references/sketch-tooling.md",
+  "gsd-core/references/sketch-variant-patterns.md",
+  "gsd-core/references/specless-probe-fallback.md",
+  "gsd-core/references/spidr-splitting.md",
+  "gsd-core/references/tdd.md",
+  "gsd-core/references/thinking-models-debug.md",
+  "gsd-core/references/thinking-models-execution.md",
+  "gsd-core/references/thinking-models-planning.md",
+  "gsd-core/references/thinking-models-research.md",
+  "gsd-core/references/thinking-models-verification.md",
+  "gsd-core/references/thinking-partner.md",
+  "gsd-core/references/ui-brand.md",
+  "gsd-core/references/ui-consideration-probe.md",
+  "gsd-core/references/universal-anti-patterns.md",
+  "gsd-core/references/untrusted-input-boundary.md",
+  "gsd-core/references/user-profiling.md",
+  "gsd-core/references/user-story-template.md",
+  "gsd-core/references/verification-overrides.md",
+  "gsd-core/references/verification-patterns.md",
+  "gsd-core/references/verify-mvp-mode.md",
+  "gsd-core/references/workstream-flag.md",
+  "gsd-core/references/worktree-branch-check.md",
+  "gsd-core/references/worktree-path-safety.md",
+  "gsd-core/templates/AI-SPEC.md",
+  "gsd-core/templates/DEBUG.md",
+  "gsd-core/templates/README.md",
+  "gsd-core/templates/SECURITY.md",
+  "gsd-core/templates/UAT.md",
+  "gsd-core/templates/UI-SPEC.md",
+  "gsd-core/templates/VALIDATION.md",
+  "gsd-core/templates/claude-md.md",
+  "gsd-core/templates/codebase/architecture.md",
+  "gsd-core/templates/codebase/concerns.md",
+  "gsd-core/templates/codebase/conventions.md",
+  "gsd-core/templates/codebase/integrations.md",
+  "gsd-core/templates/codebase/stack.md",
+  "gsd-core/templates/codebase/structure.md",
+  "gsd-core/templates/codebase/testing.md",
+  "gsd-core/templates/config.json",
+  "gsd-core/templates/context.md",
+  "gsd-core/templates/continue-here.md",
+  "gsd-core/templates/copilot-instructions.md",
+  "gsd-core/templates/debug-subagent-prompt.md",
+  "gsd-core/templates/dev-preferences.md",
+  "gsd-core/templates/discovery.md",
+  "gsd-core/templates/discussion-log.md",
+  "gsd-core/templates/milestone-archive.md",
+  "gsd-core/templates/milestone.md",
+  "gsd-core/templates/phase-prompt.md",
+  "gsd-core/templates/planner-subagent-prompt.md",
+  "gsd-core/templates/project.md",
+  "gsd-core/templates/requirements.md",
+  "gsd-core/templates/research-project/ARCHITECTURE.md",
+  "gsd-core/templates/research-project/FEATURES.md",
+  "gsd-core/templates/research-project/PITFALLS.md",
+  "gsd-core/templates/research-project/STACK.md",
+  "gsd-core/templates/research-project/SUMMARY.md",
+  "gsd-core/templates/research.md",
+  "gsd-core/templates/retrospective.md",
+  "gsd-core/templates/roadmap.md",
+  "gsd-core/templates/spec.md",
+  "gsd-core/templates/state.md",
+  "gsd-core/templates/summary-complex.md",
+  "gsd-core/templates/summary-minimal.md",
+  "gsd-core/templates/summary-standard.md",
+  "gsd-core/templates/summary.md",
+  "gsd-core/templates/user-profile.md",
+  "gsd-core/templates/user-setup.md",
+  "gsd-core/templates/verification-report.md",
+  "gsd-core/workflows/_runtime-launcher.snippet.sh",
+  "gsd-core/workflows/add-backlog.md",
+  "gsd-core/workflows/add-phase.md",
+  "gsd-core/workflows/add-tests.md",
+  "gsd-core/workflows/add-todo.md",
+  "gsd-core/workflows/ai-integration-phase.md",
+  "gsd-core/workflows/analyze-dependencies.md",
+  "gsd-core/workflows/audit-fix.md",
+  "gsd-core/workflows/audit-milestone.md",
+  "gsd-core/workflows/audit-uat.md",
+  "gsd-core/workflows/autonomous.md",
+  "gsd-core/workflows/check-todos.md",
+  "gsd-core/workflows/cleanup.md",
+  "gsd-core/workflows/code-review-fix.md",
+  "gsd-core/workflows/code-review.md",
+  "gsd-core/workflows/complete-milestone.md",
+  "gsd-core/workflows/debug.md",
+  "gsd-core/workflows/diagnose-issues.md",
+  "gsd-core/workflows/discovery-phase.md",
+  "gsd-core/workflows/discuss-phase-assumptions.md",
+  "gsd-core/workflows/discuss-phase-power.md",
+  "gsd-core/workflows/discuss-phase.md",
+  "gsd-core/workflows/discuss-phase/modes/advisor.md",
+  "gsd-core/workflows/discuss-phase/modes/all.md",
+  "gsd-core/workflows/discuss-phase/modes/analyze.md",
+  "gsd-core/workflows/discuss-phase/modes/auto.md",
+  "gsd-core/workflows/discuss-phase/modes/batch.md",
+  "gsd-core/workflows/discuss-phase/modes/chain.md",
+  "gsd-core/workflows/discuss-phase/modes/default.md",
+  "gsd-core/workflows/discuss-phase/modes/power.md",
+  "gsd-core/workflows/discuss-phase/modes/text.md",
+  "gsd-core/workflows/discuss-phase/templates/checkpoint.json",
+  "gsd-core/workflows/discuss-phase/templates/context.md",
+  "gsd-core/workflows/discuss-phase/templates/discussion-log.md",
+  "gsd-core/workflows/do.md",
+  "gsd-core/workflows/docs-update.md",
+  "gsd-core/workflows/edit-phase.md",
+  "gsd-core/workflows/eval-review.md",
+  "gsd-core/workflows/execute-phase.md",
+  "gsd-core/workflows/execute-phase/steps/codebase-drift-gate.md",
+  "gsd-core/workflows/execute-phase/steps/per-plan-worktree-gate.md",
+  "gsd-core/workflows/execute-phase/steps/post-merge-gate.md",
+  "gsd-core/workflows/execute-phase/steps/regression-gate.md",
+  "gsd-core/workflows/execute-phase/steps/worktree-recovery-policy.md",
+  "gsd-core/workflows/execute-plan.md",
+  "gsd-core/workflows/explore.md",
+  "gsd-core/workflows/extract-learnings.md",
+  "gsd-core/workflows/fast.md",
+  "gsd-core/workflows/forensics.md",
+  "gsd-core/workflows/graduation.md",
+  "gsd-core/workflows/health.md",
+  "gsd-core/workflows/help.md",
+  "gsd-core/workflows/help/modes/brief.md",
+  "gsd-core/workflows/help/modes/default.md",
+  "gsd-core/workflows/help/modes/full.md",
+  "gsd-core/workflows/help/modes/topic.md",
+  "gsd-core/workflows/import.md",
+  "gsd-core/workflows/inbox.md",
+  "gsd-core/workflows/ingest-docs.md",
+  "gsd-core/workflows/insert-phase.md",
+  "gsd-core/workflows/list-phase-assumptions.md",
+  "gsd-core/workflows/list-seeds.md",
+  "gsd-core/workflows/list-workspaces.md",
+  "gsd-core/workflows/manager.md",
+  "gsd-core/workflows/map-codebase.md",
+  "gsd-core/workflows/milestone-summary.md",
+  "gsd-core/workflows/mvp-phase.md",
+  "gsd-core/workflows/new-milestone.md",
+  "gsd-core/workflows/new-project.md",
+  "gsd-core/workflows/new-workspace.md",
+  "gsd-core/workflows/next.md",
+  "gsd-core/workflows/node-repair.md",
+  "gsd-core/workflows/note.md",
+  "gsd-core/workflows/onboard.md",
+  "gsd-core/workflows/pause-work.md",
+  "gsd-core/workflows/plan-milestone-gaps.md",
+  "gsd-core/workflows/plan-phase.md",
+  "gsd-core/workflows/plan-phase/steps/closed-phase-gate.md",
+  "gsd-core/workflows/plan-phase/steps/prd-express-path.md",
+  "gsd-core/workflows/plan-phase/steps/windows-troubleshooting.md",
+  "gsd-core/workflows/plan-review-convergence.md",
+  "gsd-core/workflows/plant-seed.md",
+  "gsd-core/workflows/pr-branch.md",
+  "gsd-core/workflows/profile-user.md",
+  "gsd-core/workflows/progress.md",
+  "gsd-core/workflows/quick.md",
+  "gsd-core/workflows/reapply-patches.md",
+  "gsd-core/workflows/remove-phase.md",
+  "gsd-core/workflows/remove-workspace.md",
+  "gsd-core/workflows/resume-project.md",
+  "gsd-core/workflows/review.md",
+  "gsd-core/workflows/scan.md",
+  "gsd-core/workflows/secure-phase.md",
+  "gsd-core/workflows/session-report.md",
+  "gsd-core/workflows/settings-advanced.md",
+  "gsd-core/workflows/settings-integrations.md",
+  "gsd-core/workflows/settings.md",
+  "gsd-core/workflows/ship.md",
+  "gsd-core/workflows/sketch-wrap-up.md",
+  "gsd-core/workflows/sketch.md",
+  "gsd-core/workflows/smart-entry.md",
+  "gsd-core/workflows/spec-phase.md",
+  "gsd-core/workflows/spike-wrap-up.md",
+  "gsd-core/workflows/spike.md",
+  "gsd-core/workflows/stats.md",
+  "gsd-core/workflows/sync-skills.md",
+  "gsd-core/workflows/thread.md",
+  "gsd-core/workflows/transition.md",
+  "gsd-core/workflows/ui-phase.md",
+  "gsd-core/workflows/ui-review.md",
+  "gsd-core/workflows/ultraplan-phase.md",
+  "gsd-core/workflows/undo.md",
+  "gsd-core/workflows/update.md",
+  "gsd-core/workflows/validate-phase.md",
+  "gsd-core/workflows/verify-phase.md",
+  "gsd-core/workflows/verify-work.md",
+  "scripts/changeset/README.md",
+  "scripts/changeset/cli.cjs",
+  "scripts/changeset/github-release-notes.cjs",
+  "scripts/changeset/lint.cjs",
+  "scripts/changeset/new.cjs",
+  "scripts/changeset/parse.cjs",
+  "scripts/changeset/render.cjs",
+  "scripts/changeset/serialize.cjs",
+  "scripts/fix-slash-commands.cjs",
+  "scripts/gen-capability-registry.cjs",
+  "scripts/gen-loop-host-contract.cjs",
+  "scripts/lib/allowlist-ratchet.cjs",
+  "scripts/lib/cli-exit.cjs",
+  "skills/gsd-ns-context/SKILL.md",
+  "skills/gsd-ns-context/skills/docs-update/SKILL.md",
+  "skills/gsd-ns-context/skills/extract-learnings/SKILL.md",
+  "skills/gsd-ns-context/skills/graphify/SKILL.md",
+  "skills/gsd-ns-context/skills/map-codebase/SKILL.md",
+  "skills/gsd-ns-context/skills/mempalace-capture/SKILL.md",
+  "skills/gsd-ns-context/skills/mempalace-recall/SKILL.md",
+  "skills/gsd-ns-ideate/SKILL.md",
+  "skills/gsd-ns-ideate/skills/capture/SKILL.md",
+  "skills/gsd-ns-ideate/skills/explore/SKILL.md",
+  "skills/gsd-ns-ideate/skills/sketch/SKILL.md",
+  "skills/gsd-ns-ideate/skills/spec-phase/SKILL.md",
+  "skills/gsd-ns-ideate/skills/spike/SKILL.md",
+  "skills/gsd-ns-manage/SKILL.md",
+  "skills/gsd-ns-manage/skills/cleanup/SKILL.md",
+  "skills/gsd-ns-manage/skills/config/SKILL.md",
+  "skills/gsd-ns-manage/skills/health/SKILL.md",
+  "skills/gsd-ns-manage/skills/help/SKILL.md",
+  "skills/gsd-ns-manage/skills/inbox/SKILL.md",
+  "skills/gsd-ns-manage/skills/manager/SKILL.md",
+  "skills/gsd-ns-manage/skills/pause-work/SKILL.md",
+  "skills/gsd-ns-manage/skills/pr-branch/SKILL.md",
+  "skills/gsd-ns-manage/skills/resume-work/SKILL.md",
+  "skills/gsd-ns-manage/skills/settings/SKILL.md",
+  "skills/gsd-ns-manage/skills/ship/SKILL.md",
+  "skills/gsd-ns-manage/skills/stats/SKILL.md",
+  "skills/gsd-ns-manage/skills/surface/SKILL.md",
+  "skills/gsd-ns-manage/skills/thread/SKILL.md",
+  "skills/gsd-ns-manage/skills/undo/SKILL.md",
+  "skills/gsd-ns-manage/skills/update/SKILL.md",
+  "skills/gsd-ns-manage/skills/workspace/SKILL.md",
+  "skills/gsd-ns-manage/skills/workstreams/SKILL.md",
+  "skills/gsd-ns-project/SKILL.md",
+  "skills/gsd-ns-project/skills/audit-milestone/SKILL.md",
+  "skills/gsd-ns-project/skills/complete-milestone/SKILL.md",
+  "skills/gsd-ns-project/skills/import/SKILL.md",
+  "skills/gsd-ns-project/skills/ingest-docs/SKILL.md",
+  "skills/gsd-ns-project/skills/milestone-summary/SKILL.md",
+  "skills/gsd-ns-project/skills/new-milestone/SKILL.md",
+  "skills/gsd-ns-project/skills/new-project/SKILL.md",
+  "skills/gsd-ns-project/skills/onboard/SKILL.md",
+  "skills/gsd-ns-project/skills/profile-user/SKILL.md",
+  "skills/gsd-ns-project/skills/review-backlog/SKILL.md",
+  "skills/gsd-ns-review/SKILL.md",
+  "skills/gsd-ns-review/skills/audit-fix/SKILL.md",
+  "skills/gsd-ns-review/skills/audit-uat/SKILL.md",
+  "skills/gsd-ns-review/skills/code-review/SKILL.md",
+  "skills/gsd-ns-review/skills/debug/SKILL.md",
+  "skills/gsd-ns-review/skills/eval-review/SKILL.md",
+  "skills/gsd-ns-review/skills/forensics/SKILL.md",
+  "skills/gsd-ns-review/skills/review/SKILL.md",
+  "skills/gsd-ns-review/skills/secure-phase/SKILL.md",
+  "skills/gsd-ns-review/skills/ui-phase/SKILL.md",
+  "skills/gsd-ns-review/skills/ui-review/SKILL.md",
+  "skills/gsd-ns-review/skills/validate-phase/SKILL.md",
+  "skills/gsd-ns-workflow/SKILL.md",
+  "skills/gsd-ns-workflow/skills/add-tests/SKILL.md",
+  "skills/gsd-ns-workflow/skills/ai-integration-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/autonomous/SKILL.md",
+  "skills/gsd-ns-workflow/skills/discuss-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/execute-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/fast/SKILL.md",
+  "skills/gsd-ns-workflow/skills/mvp-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/next/SKILL.md",
+  "skills/gsd-ns-workflow/skills/phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/plan-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/plan-review-convergence/SKILL.md",
+  "skills/gsd-ns-workflow/skills/progress/SKILL.md",
+  "skills/gsd-ns-workflow/skills/quick/SKILL.md",
+  "skills/gsd-ns-workflow/skills/spec-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/ultraplan-phase/SKILL.md",
+  "skills/gsd-ns-workflow/skills/verify-work/SKILL.md"
+]
diff --git a/tests/golden-install-tree.test.cjs b/tests/golden-install-tree.test.cjs
new file mode 100644
index 000000000..5ea28e564
--- /dev/null
+++ b/tests/golden-install-tree.test.cjs
@@ -0,0 +1,148 @@
+'use strict';
+
+/**
+ * golden-install-tree.test.cjs — file-set snapshot layer (#2267 Phase 2).
+ *
+ * Companion to tests/golden-install-parity.test.cjs. That harness hashes file
+ * CONTENT (catches a byte changing); this harness snapshots only the SORTED
+ * LIST of emitted relative paths (catches a file appearing/disappearing).
+ * Because it carries no hashes, a legitimate content-only change produces NO
+ * diff here at all, and a file being added/removed produces a small, clean,
+ * reviewable diff instead of hash noise. Both harnesses reuse the exact same
+ * exclusion set (buildParityManifest, tests/helpers/install-shared.cjs,
+ * #2266) via buildInstallTree, so the two can never diverge on which files
+ * they cover.
+ *
+ * ## UPDATE mode
+ *
+ * Run with UPDATE_INSTALL_TREE=1 to (re-)capture fixtures:
+ *   UPDATE_INSTALL_TREE=1 node --test tests/golden-install-tree.test.cjs
+ */
+
+const { test, before } = require('node:test');
+const assert = require('node:assert/strict');
+const fs = require('node:fs');
+const path = require('node:path');
+const { execFileSync } = require('node:child_process');
+
+const { cleanup } = require('./helpers.cjs');
+const { RUNTIME_META, runMinimalInstall, BUILD_SCRIPT, buildInstallTree } = require('./helpers/install-shared.cjs');
+
+// hooks/dist is gitignored and built (DEFECT.HOOKS-DIST-SCOPED-CI). The scoped
+// CI test lane does not run build:hooks, so a real install there emits no hooks/
+// dir — making the harness report "removed (N) hooks/…". Build it idempotently
+// here so the harness is lane-independent (mirrors golden-install-parity.test.cjs).
+before(() => {
+  execFileSync(process.execPath, [BUILD_SCRIPT], { encoding: 'utf-8', stdio: 'pipe' });
+});
+
+const UPDATE = process.env.UPDATE_INSTALL_TREE === '1';
+
+const FIXTURE_DIR = path.join(__dirname, 'fixtures', 'install-tree');
+
+// buildInstallTree (tests/helpers/install-shared.cjs) reuses buildParityManifest's
+// exact exclusion constants (VOLATILE_FILES, HOOK_CONFIG_FILES,
+// HOOK_CONFIG_RELATIVE_PATHS, EXCLUDED_PREFIXES) — see that module for the full
+// rationale behind each exclusion.
+
+// Ensure the fixture directory exists (needed for UPDATE mode)
+if (UPDATE) {
+  fs.mkdirSync(FIXTURE_DIR, { recursive: true });
+}
+
+function diffTree(actual, fixture) {
+  const fixtureSet = new Set(fixture);
+  const actualSet = new Set(actual);
+  const added = actual.filter((p) => !fixtureSet.has(p));
+  const removed = fixture.filter((p) => !actualSet.has(p));
+  return { added, removed };
+}
+
+const runtimes = Object.keys(RUNTIME_META);
+
+for (const runtime of runtimes) {
+  test(`install tree — ${runtime}`, async (t) => {
+    if (process.platform === 'win32') {
+      t.skip('install output is platform-specific on Windows (backslash paths); parity is asserted on macOS + Linux');
+      return;
+    }
+    const { configDir, root } = runMinimalInstall({ runtime, scope: 'global' });
+    let actual;
+    try {
+      actual = buildInstallTree(configDir, root);
+    } finally {
+      cleanup(root);
+    }
+
+    const fixturePath = path.join(FIXTURE_DIR, `${runtime}.json`);
+
+    if (UPDATE) {
+      fs.writeFileSync(fixturePath, JSON.stringify(actual, null, 2) + '\n', 'utf8');
+      process.stdout.write(`  [UPDATE] ${runtime}: wrote ${actual.length} paths → ${fixturePath}\n`);
+      return;
+    }
+
+    // Assert mode: compare against golden fixture
+    if (!fs.existsSync(fixturePath)) {
+      assert.fail(
+        `Install-tree fixture missing for runtime '${runtime}': ${fixturePath}\n` +
+        'Run UPDATE_INSTALL_TREE=1 node --test tests/golden-install-tree.test.cjs to capture.'
+      );
+    }
+
+    const fixture = JSON.parse(fs.readFileSync(fixturePath, 'utf8'));
+
+    const { added, removed } = diffTree(actual, fixture);
+
+    if (added.length > 0 || removed.length > 0) {
+      const lines = [`Install-tree mismatch for runtime '${runtime}':`];
+      if (added.length)   lines.push(`  added   (${added.length}): ${added.join(', ')}`);
+      if (removed.length) lines.push(`  removed (${removed.length}): ${removed.join(', ')}`);
+      lines.push('Run UPDATE_INSTALL_TREE=1 to recapture if the change is intentional.');
+      assert.deepEqual(actual, fixture, lines.join('\n'));
+    }
+  });
+}
+
+// #2086 (EoS/claude): claude is the reference host and the ONLY runtime with a
+// distinct LOCAL "legacy flat-commands" layout (commands/gsd-*.md + agents/gsd-*.md).
+// The loop above snapshots the GLOBAL skills layout; this snapshots the LOCAL
+// commands/agents layout's file set too (mirrors golden-install-parity.test.cjs).
+test('install tree — claude (local legacy layout)', async (t) => {
+  if (process.platform === 'win32') {
+    t.skip('install output is platform-specific on Windows (backslash paths); parity is asserted on macOS + Linux');
+    return;
+  }
+  const { configDir, root } = runMinimalInstall({ runtime: 'claude', scope: 'local' });
+  let actual;
+  try {
+    actual = buildInstallTree(configDir, root);
+  } finally {
+    cleanup(root);
+  }
+
+  const fixturePath = path.join(FIXTURE_DIR, 'claude-local.json');
+
+  if (UPDATE) {
+    fs.writeFileSync(fixturePath, JSON.stringify(actual, null, 2) + '\n', 'utf8');
+    process.stdout.write(`  [UPDATE] claude-local: wrote ${actual.length} paths → ${fixturePath}\n`);
+    return;
+  }
+
+  if (!fs.existsSync(fixturePath)) {
+    assert.fail(
+      `Install-tree fixture missing for claude-local: ${fixturePath}\n` +
+      'Run UPDATE_INSTALL_TREE=1 node --test tests/golden-install-tree.test.cjs to capture.',
+    );
+  }
+
+  const fixture = JSON.parse(fs.readFileSync(fixturePath, 'utf8'));
+  const { added, removed } = diffTree(actual, fixture);
+  if (added.length || removed.length) {
+    const lines = ['Install-tree mismatch for claude-local:'];
+    if (added.length)   lines.push(`  added   (${added.length}): ${added.join(', ')}`);
+    if (removed.length) lines.push(`  removed (${removed.length}): ${removed.join(', ')}`);
+    lines.push('Run UPDATE_INSTALL_TREE=1 to recapture if the change is intentional.');
+    assert.deepEqual(actual, fixture, lines.join('\n'));
+  }
+});
diff --git a/tests/helpers/install-shared.cjs b/tests/helpers/install-shared.cjs
index 50a6cb08b..694b85776 100644
--- a/tests/helpers/install-shared.cjs
+++ b/tests/helpers/install-shared.cjs
@@ -227,6 +227,13 @@ function buildParityManifest(configDir, root) {
   return sorted;
 }
 
+/** Sorted list of emitted relative paths for a runtime install (file-set snapshot,
+ *  #2267). Reuses buildParityManifest's exact exclusion set so the tree and the
+ *  content manifest never diverge on which files they cover. */
+function buildInstallTree(configDir, root) {
+  return Object.keys(buildParityManifest(configDir, root)).sort();
+}
+
 function simulateHookCopy(hooksSrc, hooksDest) {
   fs.mkdirSync(hooksDest, { recursive: true });
   for (const entry of fs.readdirSync(hooksSrc)) {
@@ -397,6 +404,7 @@ module.exports = {
   stripAnsi,
   walk,
   buildParityManifest,
+  buildInstallTree,
   simulateHookCopy,
   installerEnv,
   runMinimalInstall,