@opengsd/gsd-pi 1.0.1 → 1.0.2

package/src/resources/extensions/gsd/tests/integration/doctor-git.test.ts

@@ -1,954 +0,0 @@
-// GSD-2 doctor git integration tests
-import { describe, test } from 'node:test';
-import assert from 'node:assert/strict';
-/**
- * doctor-git.test.ts — Integration tests for doctor git health checks.
- *
- * Creates real temp git repos with deliberate broken state, runs runGSDDoctor,
- * and asserts correct detection and fixing of git issue codes:
- *   orphaned_auto_worktree, stale_milestone_branch,
- *   corrupt_merge_state, tracked_runtime_files,
- *   integration_branch_missing, worktree_directory_orphaned
- */
-
-import { mkdtempSync, mkdirSync, writeFileSync, rmSync, existsSync, realpathSync, readFileSync, symlinkSync, renameSync } from "node:fs";
-import { join } from "node:path";
-import { tmpdir } from "node:os";
-import { execSync, spawnSync } from "node:child_process";
-
-import { runGSDDoctor } from "../../doctor.ts";
-import { closeDatabase, insertMilestone, insertSlice, openDatabase } from "../../gsd-db.ts";
-function run(cmd: string, cwd: string): string {
-  return execSync(cmd, { cwd, stdio: ["ignore", "pipe", "pipe"], encoding: "utf-8" }).trim();
-}
-
-/** Create a temp git repo with a completed milestone M001 in roadmap. */
-function createRepoWithCompletedMilestone(): string {
-  const dir = realpathSync(mkdtempSync(join(tmpdir(), "doc-git-test-")));
-  run("git init", dir);
-  run("git config user.email test@test.com", dir);
-  run("git config user.name Test", dir);
-
-  // Initial commit
-  writeFileSync(join(dir, "README.md"), "# test\n");
-  run("git add .", dir);
-  run("git commit -m init", dir);
-  run("git branch -M main", dir);
-
-  // Create .gsd structure with milestone M001 — all slices done → complete
-  const msDir = join(dir, ".gsd", "milestones", "M001");
-  mkdirSync(msDir, { recursive: true });
-  writeFileSync(join(msDir, "ROADMAP.md"), `---
-id: M001
-title: "Test Milestone"
----
-
-# M001: Test Milestone
-
-## Vision
-Test
-
-## Success Criteria
-- Done
-
-## Slices
-- [x] **S01: Test slice** \`risk:low\` \`depends:[]\`
-  > After this: done
-
-## Boundary Map
-_None_
-`);
-  writeFileSync(join(msDir, "M001-SUMMARY.md"), `---
-id: M001
-title: "Test Milestone"
-status: complete
-completed_at: 2026-04-18T00:00:00Z
----
-
-# M001: Test Milestone
-
-Completed.
-`);
-
-  // Commit .gsd files
-  run("git add -A", dir);
-  run("git commit -m \"add milestone\"", dir);
-
-  return dir;
-}
-
-function createStashApplyConflict(): string {
-  const dir = createRepoWithCompletedMilestone();
-  writeFileSync(join(dir, "README.md"), "# local stashed work\n");
-  run('git stash push -m "local work"', dir);
-  writeFileSync(join(dir, "README.md"), "# merged milestone work\n");
-  run("git add README.md", dir);
-  run('git commit -m "feat: merged readme"', dir);
-  const apply = spawnSync("git", ["stash", "apply", "stash@{0}"], {
-    cwd: dir,
-    encoding: "utf-8",
-  });
-  if (apply.error) throw apply.error;
-  return dir;
-}
-
-/** Create a repo whose slices are done but milestone closeout is still pending. */
-function createRepoWithSlicesDoneButNoMilestoneSummary(): string {
-  const dir = realpathSync(mkdtempSync(join(tmpdir(), "doc-git-test-")));
-  run("git init", dir);
-  run("git config user.email test@test.com", dir);
-  run("git config user.name Test", dir);
-
-  writeFileSync(join(dir, "README.md"), "# test\n");
-  run("git add .", dir);
-  run("git commit -m init", dir);
-  run("git branch -M main", dir);
-
-  const msDir = join(dir, ".gsd", "milestones", "M001");
-  mkdirSync(msDir, { recursive: true });
-  writeFileSync(join(msDir, "ROADMAP.md"), `---
-id: M001
-title: "Completing Milestone"
----
-
-# M001: Completing Milestone
-
-## Vision
-Test
-
-## Success Criteria
-- Done
-
-## Slices
-- [x] **S01: Test slice** \`risk:low\` \`depends:[]\`
-  > After this: done
-
-## Boundary Map
-_None_
-`);
-
-  run("git add -A", dir);
-  run("git commit -m \"add completing milestone\"", dir);
-
-  return dir;
-}
-
-/** Write a .gsd/PREFERENCES.md with the given git isolation mode. */
-function writePreferencesFile(dir: string, isolation: "none" | "worktree" | "branch"): void {
-  const gsdDir = join(dir, ".gsd");
-  mkdirSync(gsdDir, { recursive: true });
-  writeFileSync(join(gsdDir, "PREFERENCES.md"), `---\ngit:\n  isolation: "${isolation}"\n---\n`);
-}
-
-/** Create a repo with an in-progress milestone. */
-function createRepoWithActiveMilestone(): string {
-  const dir = realpathSync(mkdtempSync(join(tmpdir(), "doc-git-test-")));
-  run("git init", dir);
-  run("git config user.email test@test.com", dir);
-  run("git config user.name Test", dir);
-
-  writeFileSync(join(dir, "README.md"), "# test\n");
-  run("git add .", dir);
-  run("git commit -m init", dir);
-  run("git branch -M main", dir);
-
-  const msDir = join(dir, ".gsd", "milestones", "M001");
-  mkdirSync(msDir, { recursive: true });
-  writeFileSync(join(msDir, "ROADMAP.md"), `---
-id: M001
-title: "Active Milestone"
----
-
-# M001: Active Milestone
-
-## Vision
-Test
-
-## Success Criteria
-- Done
-
-## Slices
-- [ ] **S01: Test slice** \`risk:low\` \`depends:[]\`
-  > After this: done
-
-## Boundary Map
-_None_
-`);
-
-  run("git add -A", dir);
-  run("git commit -m \"add milestone\"", dir);
-
-  return dir;
-}
-
-describe('doctor-git', async () => {
-  const cleanups: string[] = [];
-
-  try {
-    // ─── Test 1: Orphaned worktree detection & fix ─────────────────────
-    // Skip on Windows: git worktree path resolution on Windows temp dirs
-    // uses UNC/8.3 forms that don't survive path normalization. The source
-    // logic is correct (tested on macOS/Linux) — the test infra doesn't
-    // produce matching paths on Windows CI.
-    if (process.platform !== "win32") {
-    test('orphaned_auto_worktree', async () => {
-      const dir = createRepoWithCompletedMilestone();
-      cleanups.push(dir);
-
-      // Create worktree with milestone/M001 branch under .gsd/worktrees/
-      mkdirSync(join(dir, ".gsd", "worktrees"), { recursive: true });
-      run("git worktree add -b milestone/M001 .gsd/worktrees/M001", dir);
-
-      const detect = await runGSDDoctor(dir, { isolationMode: "worktree" });
-      const orphanIssues = detect.issues.filter(i => i.code === "orphaned_auto_worktree");
-      assert.ok(orphanIssues.length > 0, "detects orphaned worktree");
-      assert.deepStrictEqual(orphanIssues[0]?.unitId, "M001", "orphaned worktree unitId is M001");
-
-      const fixed = await runGSDDoctor(dir, { fix: true, isolationMode: "worktree" });
-      assert.ok(fixed.fixesApplied.some(f => f.includes("removed orphaned worktree")), "fix removes orphaned worktree");
-
-      // Verify worktree is gone
-      const wtList = run("git worktree list", dir);
-      assert.ok(!wtList.includes("milestone/M001"), "worktree no longer listed after fix");
-    });
-    } else {
-    }
-
-    // ─── Test 1b: Orphaned worktree fix when cwd is inside worktree (#1946) ──
-    // Reproduces the deadlock: if process.cwd() is inside the orphaned worktree,
-    // the doctor must chdir out before removing it — not skip the removal.
-    if (process.platform !== "win32") {
-    console.log("\n=== orphaned_auto_worktree (cwd inside worktree) ===");
-    {
-      const dir = createRepoWithCompletedMilestone();
-      cleanups.push(dir);
-
-      // Create worktree with milestone/M001 branch under .gsd/worktrees/
-      mkdirSync(join(dir, ".gsd", "worktrees"), { recursive: true });
-      run("git worktree add -b milestone/M001 .gsd/worktrees/M001", dir);
-
-      const wtPath = realpathSync(join(dir, ".gsd", "worktrees", "M001"));
-
-      // Simulate the deadlock: set cwd inside the orphaned worktree
-      const previousCwd = process.cwd();
-      process.chdir(wtPath);
-      try {
-        const fixed = await runGSDDoctor(dir, { fix: true, isolationMode: "worktree" });
-
-        // The fix must NOT skip removal — it should chdir out and remove
-        assert.ok(
-          !fixed.fixesApplied.some(f => f.includes("skipped removing worktree")),
-          "does NOT skip removal when cwd is inside worktree",
-        );
-        assert.ok(
-          fixed.fixesApplied.some(f => f.includes("removed orphaned worktree")),
-          "removes orphaned worktree even when cwd was inside it",
-        );
-
-        // Verify worktree is gone
-        const wtList = run("git worktree list", dir);
-        assert.ok(!wtList.includes("milestone/M001"), "worktree removed after fix with cwd inside");
-
-        // Verify cwd was moved out (should be basePath, not still inside worktree)
-        const newCwd = process.cwd();
-        assert.ok(
-          !newCwd.startsWith(wtPath),
-          "cwd moved out of worktree after fix",
-        );
-      } finally {
-        // Restore cwd — the worktree dir may be gone, so chdir to previousCwd
-        try { process.chdir(previousCwd); } catch { process.chdir(dir); }
-      }
-    }
-    } else {
-      console.log("\n=== orphaned_auto_worktree (cwd inside worktree — skipped on Windows) ===");
-    }
-
-    // ─── Test 2: Stale milestone branch detection & fix ────────────────
-    // Skip on Windows: git branch glob matching and path resolution
-    // behave differently in Windows temp dirs.
-    if (process.platform !== "win32") {
-    test('stale_milestone_branch', async () => {
-      const dir = createRepoWithCompletedMilestone();
-      cleanups.push(dir);
-
-      // Create a milestone/M001 branch (no worktree)
-      run("git branch milestone/M001", dir);
-
-      const detect = await runGSDDoctor(dir, { isolationMode: "worktree" });
-      const staleIssues = detect.issues.filter(i => i.code === "stale_milestone_branch");
-      assert.ok(staleIssues.length > 0, "detects stale milestone branch");
-      assert.deepStrictEqual(staleIssues[0]?.unitId, "M001", "stale branch unitId is M001");
-
-      const fixed = await runGSDDoctor(dir, { fix: true, isolationMode: "worktree" });
-      assert.ok(fixed.fixesApplied.some(f => f.includes("deleted stale branch")), "fix deletes stale branch");
-
-      // Verify branch is gone
-      const branches = run("git branch --list milestone/*", dir);
-      assert.ok(!branches.includes("milestone/M001"), "branch gone after fix");
-    });
-    } else {
-    }
-
-    // ─── Test 3: Corrupt merge state detection & fix ───────────────────
-    test('corrupt_merge_state', async () => {
-      const dir = createRepoWithCompletedMilestone();
-      cleanups.push(dir);
-
-      // Inject MERGE_HEAD into .git
-      const headHash = run("git rev-parse HEAD", dir);
-      writeFileSync(join(dir, ".git", "MERGE_HEAD"), headHash + "\n");
-
-      const detect = await runGSDDoctor(dir);
-      const mergeIssues = detect.issues.filter(i => i.code === "corrupt_merge_state");
-      assert.ok(mergeIssues.length > 0, "detects corrupt merge state");
-
-      const fixed = await runGSDDoctor(dir, { fix: true });
-      assert.ok(fixed.fixesApplied.some(f => f.includes("cleaned merge state")), "fix cleans merge state");
-
-      // Verify MERGE_HEAD is gone
-      assert.ok(!existsSync(join(dir, ".git", "MERGE_HEAD")), "MERGE_HEAD removed after fix");
-    });
-
-    test('unresolved_git_conflicts is manual-only and preserves conflict state', async () => {
-      const dir = createStashApplyConflict();
-      cleanups.push(dir);
-      assert.equal(existsSync(join(dir, ".git", "MERGE_HEAD")), false, "stash apply conflict should not require MERGE_HEAD");
-
-      const detect = await runGSDDoctor(dir);
-      const conflictIssues = detect.issues.filter(i => i.code === "unresolved_git_conflicts");
-      assert.equal(conflictIssues.length, 1, "detects unresolved Git conflict index");
-      assert.equal(conflictIssues[0]?.severity, "error");
-      assert.equal(conflictIssues[0]?.fixable, false);
-      assert.match(conflictIssues[0]?.message ?? "", /README\.md/);
-
-      const fixed = await runGSDDoctor(dir, { fix: true });
-      assert.ok(
-        !fixed.fixesApplied.some((fix) => fix.includes("cleaned merge state")),
-        "doctor fix must not reset conflict files",
-      );
-      assert.match(run("git diff --name-only --diff-filter=U", dir), /README\.md/, "conflict remains for manual resolution");
-    });
-
-    // ─── Test 4: Tracked runtime files detection & fix ─────────────────
-    test('tracked_runtime_files', async () => {
-      const dir = createRepoWithCompletedMilestone();
-      cleanups.push(dir);
-
-      // Force-add a runtime file
-      const activityDir = join(dir, ".gsd", "activity");
-      mkdirSync(activityDir, { recursive: true });
-      writeFileSync(join(activityDir, "test.log"), "log data\n");
-      run("git add -f .gsd/activity/test.log", dir);
-      run("git commit -m \"track runtime file\"", dir);
-
-      const detect = await runGSDDoctor(dir);
-      const trackedIssues = detect.issues.filter(i => i.code === "tracked_runtime_files");
-      assert.ok(trackedIssues.length > 0, "detects tracked runtime files");
-
-      const fixed = await runGSDDoctor(dir, { fix: true });
-      assert.ok(fixed.fixesApplied.some(f => f.includes("untracked")), "fix untracks runtime files");
-
-      // Verify file is no longer tracked
-      const tracked = run("git ls-files .gsd/activity/", dir);
-      assert.deepStrictEqual(tracked, "", "runtime file untracked after fix");
-    });
-
-    // ─── Test 5: Non-git directory — graceful degradation ──────────────
-    test('non-git directory', async () => {
-      const dir = realpathSync(mkdtempSync(join(tmpdir(), "doc-git-test-")));
-      cleanups.push(dir);
-
-      // Create minimal .gsd structure (no git)
-      mkdirSync(join(dir, ".gsd"), { recursive: true });
-
-      const result = await runGSDDoctor(dir);
-      const gitIssues = result.issues.filter(i =>
-        ["orphaned_auto_worktree", "stale_milestone_branch", "corrupt_merge_state", "tracked_runtime_files"].includes(i.code)
-      );
-      assert.deepStrictEqual(gitIssues.length, 0, "no git issues in non-git directory");
-      // Should not throw — reaching here means no crash
-      assert.ok(true, "non-git directory does not crash");
-    });
-
-    // ─── Test 6: Active worktree NOT flagged (false positive prevention) ─
-    if (process.platform !== "win32") {
-    test('active worktree safety', async () => {
-      const dir = createRepoWithActiveMilestone();
-      cleanups.push(dir);
-
-      // Create worktree for in-progress milestone under .gsd/worktrees/
-      mkdirSync(join(dir, ".gsd", "worktrees"), { recursive: true });
-      run("git worktree add -b milestone/M001 .gsd/worktrees/M001", dir);
-
-      const detect = await runGSDDoctor(dir, { isolationMode: "worktree" });
-      const orphanIssues = detect.issues.filter(i => i.code === "orphaned_auto_worktree");
-      assert.deepStrictEqual(orphanIssues.length, 0, "active worktree NOT flagged as orphaned");
-    });
-    } else {
-    }
-
-    // ─── Test 6b: completing-milestone worktree NOT flagged ────────────
-    if (process.platform !== "win32") {
-    test('completing-milestone worktree safety (DB-backed, no summary)', async () => {
-      const dir = createRepoWithSlicesDoneButNoMilestoneSummary();
-      cleanups.push(dir);
-
-      mkdirSync(join(dir, ".gsd", "worktrees"), { recursive: true });
-      run("git worktree add -b milestone/M001 .gsd/worktrees/M001", dir);
-
-      const dbPath = join(dir, ".gsd", "gsd.db");
-      assert.equal(openDatabase(dbPath), true, "opens gsd.db");
-      try {
-        insertMilestone({ id: "M001", title: "Completing Milestone", status: "active" });
-        insertSlice({ id: "S01", milestoneId: "M001", title: "Test slice", status: "complete", risk: "low", depends: [] });
-
-        const detect = await runGSDDoctor(dir, { isolationMode: "worktree" });
-        const orphanIssues = detect.issues.filter(i => i.code === "orphaned_auto_worktree");
-        assert.deepStrictEqual(orphanIssues.length, 0, "completing milestone NOT flagged as orphaned");
-      } finally {
-        closeDatabase();
-      }
-    });
-    } else {
-    }
-
-    // ─── Test 7: none-mode skips orphaned worktree check ───────────────
-    // NOTE: loadEffectiveGSDPreferences() resolves PROJECT_PREFERENCES_PATH
-    // at module load time from process.cwd(). We write the prefs file to
-    // the test runner's cwd .gsd/PREFERENCES.md and clean up afterwards.
-    if (process.platform !== "win32") {
-    test('none-mode skips orphaned worktree', async () => {
-      const dir = createRepoWithCompletedMilestone();
-      cleanups.push(dir);
-
-      // Create worktree with milestone/M001 branch under .gsd/worktrees/
-      mkdirSync(join(dir, ".gsd", "worktrees"), { recursive: true });
-      run("git worktree add -b milestone/M001 .gsd/worktrees/M001", dir);
-
-      const result = await runGSDDoctor(dir, { isolationMode: "none" });
-      const orphanIssues = result.issues.filter(i => i.code === "orphaned_auto_worktree");
-      assert.deepStrictEqual(orphanIssues.length, 0, "none-mode: orphaned worktree NOT detected");
-    });
-    } else {
-    }
-
-    // ─── Test 8: none-mode skips stale branch check ────────────────────
-    if (process.platform !== "win32") {
-    test('none-mode skips stale branch', async () => {
-      const dir = createRepoWithCompletedMilestone();
-      cleanups.push(dir);
-
-      // Create a milestone/M001 branch (no worktree)
-      run("git branch milestone/M001", dir);
-
-      const result = await runGSDDoctor(dir, { isolationMode: "none" });
-      const staleIssues = result.issues.filter(i => i.code === "stale_milestone_branch");
-      assert.deepStrictEqual(staleIssues.length, 0, "none-mode: stale branch NOT detected");
-    });
-    } else {
-    }
-
-    // ─── Test: Integration branch missing ──────────────────────────────
-    if (process.platform !== "win32") {
-    test('integration_branch_missing', async () => {
-      const dir = createRepoWithActiveMilestone();
-      cleanups.push(dir);
-
-      // Write integration branch metadata for M001 pointing to a non-existent branch
-      const metaPath = join(dir, ".gsd", "milestones", "M001", "M001-META.json");
-      writeFileSync(metaPath, JSON.stringify({ integrationBranch: "feat/does-not-exist" }, null, 2));
-
-      const detect = await runGSDDoctor(dir);
-      const missingBranchIssues = detect.issues.filter(i => i.code === "integration_branch_missing");
-      assert.ok(missingBranchIssues.length > 0, "detects missing integration branch");
-      assert.ok(
-        missingBranchIssues[0]?.message.includes("feat/does-not-exist"),
-        "message includes the missing branch name",
-      );
-      assert.deepStrictEqual(missingBranchIssues[0]?.fixable, true, "integration_branch_missing is auto-fixable via fallback");
-      assert.deepStrictEqual(missingBranchIssues[0]?.severity, "warning", "severity is warning (fallback available)");
-    });
-    } else {
-    }
-
-    // ─── Test: Integration branch present — no false positive ──────────
-    if (process.platform !== "win32") {
-    test('integration_branch_missing (no false positive)', async () => {
-      const dir = createRepoWithActiveMilestone();
-      cleanups.push(dir);
-
-      // Write integration branch metadata for M001 pointing to "main" (which exists)
-      const metaPath = join(dir, ".gsd", "milestones", "M001", "M001-META.json");
-      writeFileSync(metaPath, JSON.stringify({ integrationBranch: "main" }, null, 2));
-
-      const detect = await runGSDDoctor(dir);
-      const missingBranchIssues = detect.issues.filter(i => i.code === "integration_branch_missing");
-      assert.deepStrictEqual(missingBranchIssues.length, 0, "existing integration branch NOT flagged");
-    });
-    } else {
-    }
-
-    // ─── Test: Orphaned worktree directory ─────────────────────────────
-    test('integration_branch_missing: stale metadata with detected fallback', async () => {
-      const dir = createRepoWithActiveMilestone();
-      cleanups.push(dir);
-
-      const metaPath = join(dir, ".gsd", "milestones", "M001", "M001-META.json");
-      writeFileSync(metaPath, JSON.stringify({ integrationBranch: "feat/does-not-exist" }, null, 2));
-
-      const detect = await runGSDDoctor(dir);
-      const missingBranchIssues = detect.issues.filter(i => i.code === "integration_branch_missing");
-      assert.deepStrictEqual(missingBranchIssues.length, 1, "reports one stale integration branch issue");
-      assert.deepStrictEqual(missingBranchIssues[0]?.severity, "warning", "stale metadata is warning when a fallback branch exists");
-      assert.deepStrictEqual(missingBranchIssues[0]?.fixable, true, "stale metadata becomes auto-fixable when fallback exists");
-      assert.ok(
-        missingBranchIssues[0]?.message.includes("feat/does-not-exist") &&
-        missingBranchIssues[0]?.message.includes("main"),
-        "warning mentions stale recorded branch and detected fallback branch",
-      );
-
-      const fixed = await runGSDDoctor(dir, { fix: true });
-      assert.ok(
-        fixed.fixesApplied.some(f => f.includes('updated integration branch for M001 to "main"')),
-        "doctor fix rewrites stale integration branch metadata to detected fallback branch",
-      );
-
-      const repairedMeta = JSON.parse(readFileSync(metaPath, "utf-8"));
-      assert.deepStrictEqual(repairedMeta.integrationBranch, "main", "metadata rewritten to detected fallback branch");
-    });
-
-    test('integration_branch_missing: stale metadata with configured fallback', async () => {
-      const dir = createRepoWithActiveMilestone();
-      cleanups.push(dir);
-
-      run("git branch trunk", dir);
-      writeFileSync(join(dir, ".gsd", "PREFERENCES.md"), `---\ngit:\n  isolation: "worktree"\n  main_branch: "trunk"\n---\n`);
-
-      const metaPath = join(dir, ".gsd", "milestones", "M001", "M001-META.json");
-      writeFileSync(metaPath, JSON.stringify({ integrationBranch: "feat/does-not-exist" }, null, 2));
-
-      const previousCwd = process.cwd();
-      process.chdir(dir);
-      try {
-        const detect = await runGSDDoctor(dir);
-        const missingBranchIssues = detect.issues.filter(i => i.code === "integration_branch_missing");
-        assert.deepStrictEqual(missingBranchIssues.length, 1, "configured fallback still reports one stale integration branch issue");
-        assert.deepStrictEqual(missingBranchIssues[0]?.severity, "warning", "configured fallback keeps stale metadata at warning severity");
-        assert.deepStrictEqual(missingBranchIssues[0]?.fixable, true, "configured fallback remains auto-fixable");
-        assert.ok(
-          missingBranchIssues[0]?.message.includes("feat/does-not-exist") &&
-          missingBranchIssues[0]?.message.includes("trunk"),
-          "warning mentions stale recorded branch and configured fallback branch",
-        );
-
-        const fixed = await runGSDDoctor(dir, { fix: true });
-        assert.ok(
-          fixed.fixesApplied.some(f => f.includes('updated integration branch for M001 to "trunk"')),
-          "doctor fix rewrites stale metadata to configured fallback branch",
-        );
-      } finally {
-        process.chdir(previousCwd);
-      }
-
-      const repairedMeta = JSON.parse(readFileSync(metaPath, "utf-8"));
-      assert.deepStrictEqual(repairedMeta.integrationBranch, "trunk", "metadata rewritten to configured fallback branch");
-    });
-
-    if (process.platform !== "win32") {
-    test('worktree_directory_orphaned', async () => {
-      const dir = createRepoWithActiveMilestone();
-      cleanups.push(dir);
-
-      // Create a worktrees/ dir with an entry that is NOT in git worktree list
-      const orphanDir = join(dir, ".gsd", "worktrees", "orphan-feature");
-      mkdirSync(orphanDir, { recursive: true });
-      writeFileSync(join(orphanDir, "some-file.txt"), "leftover content\n");
-
-      const detect = await runGSDDoctor(dir);
-      const orphanDirIssues = detect.issues.filter(i => i.code === "worktree_directory_orphaned");
-      assert.ok(orphanDirIssues.length > 0, "detects orphaned worktree directory");
-      assert.ok(
-        orphanDirIssues[0]?.message.includes("orphan-feature"),
-        "message includes the orphaned directory name",
-      );
-      assert.ok(orphanDirIssues[0]?.fixable === true, "worktree_directory_orphaned is fixable");
-
-      const fixed = await runGSDDoctor(dir, { fix: true });
-      assert.ok(
-        fixed.fixesApplied.some(f => f.includes("removed orphaned worktree directory")),
-        "fix removes orphaned worktree directory",
-      );
-      assert.ok(!existsSync(orphanDir), "orphaned directory removed after fix");
-    });
-    } else {
-    }
-
-    // ─── Test: Registered worktree NOT flagged as orphaned ─────────────
-    if (process.platform !== "win32") {
-    test('worktree_directory_orphaned (registered worktree not flagged)', async () => {
-      const dir = createRepoWithActiveMilestone();
-      cleanups.push(dir);
-
-      // Create a real registered worktree under .gsd/worktrees/
-      mkdirSync(join(dir, ".gsd", "worktrees"), { recursive: true });
-      run("git worktree add -b worktree/feature-1 .gsd/worktrees/feature-1", dir);
-
-      const detect = await runGSDDoctor(dir);
-      const orphanDirIssues = detect.issues.filter(i => i.code === "worktree_directory_orphaned");
-      assert.deepStrictEqual(orphanDirIssues.length, 0, "registered worktree NOT flagged as orphaned");
-    });
-    } else {
-    }
-
-    // ─── Test 9: none-mode still detects corrupt merge state ───────────
-    test('none-mode keeps corrupt merge state', async () => {
-      const dir = createRepoWithCompletedMilestone();
-      cleanups.push(dir);
-
-      // Inject MERGE_HEAD into .git
-      const headHash = run("git rev-parse HEAD", dir);
-      writeFileSync(join(dir, ".git", "MERGE_HEAD"), headHash + "\n");
-
-      const result = await runGSDDoctor(dir, { isolationMode: "none" });
-      const mergeIssues = result.issues.filter(i => i.code === "corrupt_merge_state");
-      assert.ok(mergeIssues.length > 0, "none-mode: corrupt merge state IS detected");
-    });
-
-    // ─── Test 10: none-mode still detects tracked runtime files ────────
-    test('none-mode keeps tracked runtime files', async () => {
-      const dir = createRepoWithCompletedMilestone();
-      cleanups.push(dir);
-
-      // Force-add a runtime file
-      const activityDir = join(dir, ".gsd", "activity");
-      mkdirSync(activityDir, { recursive: true });
-      writeFileSync(join(activityDir, "test.log"), "log data\n");
-      run("git add -f .gsd/activity/test.log", dir);
-      run("git commit -m \"track runtime file\"", dir);
-
-      const result = await runGSDDoctor(dir, { isolationMode: "none" });
-      const trackedIssues = result.issues.filter(i => i.code === "tracked_runtime_files");
-      assert.ok(trackedIssues.length > 0, "none-mode: tracked runtime files IS detected");
-    });
-
-    // ─── Test: Symlinked .gsd does not cause false orphan detection ────
-    if (process.platform !== "win32") {
-    test('worktree_directory_orphaned (symlinked .gsd not false-positive)', async () => {
-      const dir = createRepoWithActiveMilestone();
-      cleanups.push(dir);
-
-      // Move .gsd to an external location and replace with a symlink.
-      // This simulates the ~/.gsd/projects/<hash> layout where .gsd is a symlink.
-      const externalGsd = join(realpathSync(mkdtempSync(join(tmpdir(), "doc-git-symlink-"))), "gsd-data");
-      cleanups.push(externalGsd);
-      renameSync(join(dir, ".gsd"), externalGsd);
-      symlinkSync(externalGsd, join(dir, ".gsd"));
-
-      // Create a real registered worktree under the (now symlinked) .gsd/worktrees/
-      mkdirSync(join(dir, ".gsd", "worktrees"), { recursive: true });
-      run("git worktree add -b worktree/symlink-test .gsd/worktrees/symlink-test", dir);
-
-      const detect = await runGSDDoctor(dir);
-      const orphanDirIssues = detect.issues.filter(i => i.code === "worktree_directory_orphaned");
-      assert.deepStrictEqual(orphanDirIssues.length, 0, "registered worktree via symlinked .gsd NOT flagged as orphaned");
-    });
-    } else {
-    }
-
-    // ─── Test: worktree_branch_merged detection & fix ──────────────────
-    if (process.platform !== "win32") {
-    test('worktree_branch_merged', async () => {
-      const dir = createRepoWithActiveMilestone();
-      cleanups.push(dir);
-
-      // Create a worktree, make a commit, then merge the branch into main
-      mkdirSync(join(dir, ".gsd", "worktrees"), { recursive: true });
-      run("git worktree add -b worktree/merged-feature .gsd/worktrees/merged-feature", dir);
-      const wtPath = join(dir, ".gsd", "worktrees", "merged-feature");
-      writeFileSync(join(wtPath, "feature.txt"), "feature\n");
-      run("git add -A", wtPath);
-      run("git -c user.email=test@test.com -c user.name=Test commit -m \"feature work\"", wtPath);
-
-      // Merge the worktree branch into main
-      run("git merge worktree/merged-feature --no-edit", dir);
-
-      const detect = await runGSDDoctor(dir);
-      const mergedIssues = detect.issues.filter(i => i.code === "worktree_branch_merged");
-      assert.ok(mergedIssues.length > 0, "detects merged worktree branch");
-      assert.ok(mergedIssues[0]?.message.includes("safe to remove"), "message says safe to remove");
-      assert.ok(mergedIssues[0]?.fixable === true, "merged worktree is fixable");
-
-      // Fix should remove the worktree
-      const fixed = await runGSDDoctor(dir, { fix: true });
-      assert.ok(fixed.fixesApplied.some(f => f.includes("removed merged worktree")), "fix removes merged worktree");
-      assert.ok(!existsSync(wtPath), "worktree directory removed after fix");
-    });
-    } else {
-    }
-
-    // ─── Test: merged milestone/* worktree removes milestone branch ────
-    if (process.platform !== "win32") {
-    test('worktree_branch_merged (milestone branch cleanup)', async () => {
-      const dir = createRepoWithActiveMilestone();
-      cleanups.push(dir);
-
-      mkdirSync(join(dir, ".gsd", "worktrees"), { recursive: true });
-      run("git worktree add -b milestone/M001 .gsd/worktrees/M001", dir);
-      const wtPath = join(dir, ".gsd", "worktrees", "M001");
-      writeFileSync(join(wtPath, "feature.txt"), "feature\n");
-      run("git add -A", wtPath);
-      run("git -c user.email=test@test.com -c user.name=Test commit -m \"feature work\"", wtPath);
-      run("git merge milestone/M001 --no-edit", dir);
-
-      const fixed = await runGSDDoctor(dir, { fix: true });
-      assert.ok(fixed.fixesApplied.some(f => f.includes("removed merged worktree")), "fix removes merged milestone worktree");
-      assert.ok(!existsSync(wtPath), "milestone worktree directory removed after fix");
-
-      const branches = run("git branch --list milestone/M001", dir);
-      assert.deepStrictEqual(branches, "", "milestone/M001 branch deleted after merged worktree cleanup");
-    });
-    } else {
-    }
-
-    // ─── Test: merged current worktree is not self-removed ─────────────
-    if (process.platform !== "win32") {
-    test('worktree_branch_merged (current worktree not removed)', async () => {
-      const dir = createRepoWithActiveMilestone();
-      cleanups.push(dir);
-
-      mkdirSync(join(dir, ".gsd", "worktrees"), { recursive: true });
-      run("git worktree add -b worktree/current-merged .gsd/worktrees/current-merged", dir);
-      const wtPath = realpathSync(join(dir, ".gsd", "worktrees", "current-merged"));
-      writeFileSync(join(wtPath, "current.txt"), "current worktree\n");
-      run("git add -A", wtPath);
-      run("git -c user.email=test@test.com -c user.name=Test commit -m \"current worktree\"", wtPath);
-      run("git merge worktree/current-merged --no-edit", dir);
-
-      const previousCwd = process.cwd();
-      process.chdir(wtPath);
-      try {
-        const fixed = await runGSDDoctor(wtPath, { fix: true });
-        const mergedIssues = fixed.issues.filter(i => i.code === "worktree_branch_merged");
-
-        assert.ok(mergedIssues.length > 0, "detects merged current worktree branch");
-        assert.ok(
-          !fixed.fixesApplied.some(f => f.includes("removed merged worktree")),
-          "does not remove the active current worktree",
-        );
-        assert.ok(existsSync(wtPath), "current worktree directory still exists after doctor --fix");
-      } finally {
-        try { process.chdir(previousCwd); } catch { process.chdir(dir); }
-      }
-    });
-    } else {
-    }
-
-    // ─── Test: worktree_branch_merged NOT flagged for unmerged worktree ─
-    if (process.platform !== "win32") {
-    test('worktree_branch_merged (no false positive)', async () => {
-      const dir = createRepoWithActiveMilestone();
-      cleanups.push(dir);
-
-      mkdirSync(join(dir, ".gsd", "worktrees"), { recursive: true });
-      run("git worktree add -b worktree/active-feature .gsd/worktrees/active-feature", dir);
-      const wtPath = join(dir, ".gsd", "worktrees", "active-feature");
-      writeFileSync(join(wtPath, "wip.txt"), "work in progress\n");
-      run("git add -A", wtPath);
-      run("git -c user.email=test@test.com -c user.name=Test commit -m \"wip\"", wtPath);
-
-      // Do NOT merge — branch is ahead of main
-      const detect = await runGSDDoctor(dir);
-      const mergedIssues = detect.issues.filter(i => i.code === "worktree_branch_merged");
-      assert.deepStrictEqual(mergedIssues.length, 0, "unmerged worktree NOT flagged as merged");
-    });
-    } else {
-    }
-
-    // ─── Test: legacy_slice_branches now fixable ───────────────────────
-    if (process.platform !== "win32") {
-    test('legacy_slice_branches (fixable)', async () => {
-      const dir = createRepoWithActiveMilestone();
-      cleanups.push(dir);
-
-      // Create legacy gsd/M001/S01 branches
-      run("git branch gsd/M001/S01", dir);
-      run("git branch gsd/M001/S02", dir);
-      // Active quick branches share gsd/*/* shape and must NOT be deleted.
-      run("git branch gsd/quick/1-fix-typo", dir);
-
-      const detect = await runGSDDoctor(dir);
-      const legacyIssues = detect.issues.filter(i => i.code === "legacy_slice_branches");
-      assert.ok(legacyIssues.length > 0, "detects legacy slice branches");
-      assert.ok(legacyIssues[0]?.fixable === true, "legacy branches are fixable");
-
-      const fixed = await runGSDDoctor(dir, { fix: true });
-      assert.ok(fixed.fixesApplied.some(f => f.includes("legacy slice branch")), "fix deletes legacy branches");
-
-      // Verify branches are gone
-      const remaining = run("git branch --list gsd/*/*", dir);
-      assert.deepStrictEqual(remaining, "gsd/quick/1-fix-typo", "quick branch preserved; legacy branches removed");
-    });
-    } else {
-    }
-
-    // ─── Test: stale_uncommitted_changes detection & auto-snapshot ──────
-    test('stale_uncommitted_changes (detected and auto-committed)', async () => {
-      const dir = createRepoWithActiveMilestone();
-      cleanups.push(dir);
-
-      // Make the last commit appear old by amending its date to 45 min ago
-      const pastDate = new Date(Date.now() - 45 * 60 * 1000).toISOString();
-      run(`git commit --amend --no-edit --date="${pastDate}"`, dir);
-      // Also set committer date so git log %ct reflects it
-      execSync(`git commit --amend --no-edit`, {
-        cwd: dir,
-        stdio: ["ignore", "pipe", "pipe"],
-        encoding: "utf-8",
-        env: { ...process.env, GIT_COMMITTER_DATE: pastDate },
-      });
-
-      // Modify an already-tracked file (nativeAddTracked uses git add -u,
-      // which only stages tracked files — new untracked files are not staged)
-      writeFileSync(join(dir, "README.md"), "# test\nmodified content\n");
-
-      const detect = await runGSDDoctor(dir);
-      const staleIssues = detect.issues.filter(i => i.code === "stale_uncommitted_changes");
-      assert.ok(staleIssues.length > 0, "detects stale uncommitted changes");
-      assert.ok(staleIssues[0]?.message.includes("minute"), "message mentions minutes");
-      assert.ok(staleIssues[0]?.fixable === true, "stale uncommitted changes is fixable");
-
-      // Fix should create a gsd snapshot commit
-      const fixed = await runGSDDoctor(dir, { fix: true });
-      assert.ok(
-        fixed.fixesApplied.some(f => f.includes("gsd snapshot")),
-        "fix creates a gsd snapshot commit",
-      );
-
-      // Verify the snapshot commit was created with the gsd snapshot tag
-      const log = run("git log -1 --oneline", dir);
-      assert.ok(log.includes("gsd snapshot"), "commit is tagged with gsd snapshot");
-    });
-
-    test('stale_uncommitted_changes (skips snapshot when tracked changes contain conflict markers)', async () => {
-      const dir = createRepoWithActiveMilestone();
-      cleanups.push(dir);
-
-      const pastDate = new Date(Date.now() - 45 * 60 * 1000).toISOString();
-      run(`git commit --amend --no-edit --date="${pastDate}"`, dir);
-      execSync(`git commit --amend --no-edit`, {
-        cwd: dir,
-        stdio: ["ignore", "pipe", "pipe"],
-        encoding: "utf-8",
-        env: { ...process.env, GIT_COMMITTER_DATE: pastDate },
-      });
-
-      writeFileSync(join(dir, "README.md"), [
-        "# test",
-        "<<<<<<< Updated upstream",
-        "modified content",
-        "=======",
-        "stashed content",
-        ">>>>>>> Stashed changes",
-        "",
-      ].join("\n"));
-
-      const commitsBefore = run("git rev-list --count HEAD", dir);
-      const fixed = await runGSDDoctor(dir, { fix: true });
-      const conflictIssues = fixed.issues.filter(
-        i => i.code === ("conflict_markers_in_tracked_files" as typeof i.code),
-      );
-
-      assert.equal(conflictIssues.length, 1, "detects conflict markers before snapshotting");
-      assert.equal(conflictIssues[0]?.severity, "error", "conflict marker issue blocks automation");
-      assert.equal(conflictIssues[0]?.fixable, false, "conflict marker issue requires manual resolution");
-      assert.ok(
-        fixed.fixesApplied.some(f => f.includes("gsd snapshot skipped")),
-        "fix reports skipped snapshot",
-      );
-
-      const commitsAfter = run("git rev-list --count HEAD", dir);
-      assert.equal(commitsAfter, commitsBefore, "no snapshot commit is created");
-      assert.equal(run("git diff --cached --name-only", dir), "", "no files are staged");
-      assert.match(run("git status --short", dir), /M README\.md/m, "tracked file remains modified");
-    });
-
-    // ─── Test: stale_uncommitted_changes NOT flagged when recent commit ──
-    test('stale_uncommitted_changes (no false positive on recent commit)', async () => {
-      const dir = createRepoWithActiveMilestone();
-      cleanups.push(dir);
-
-      // Create uncommitted changes (but last commit is fresh — just created)
-      writeFileSync(join(dir, "fresh-dirty.txt"), "recent changes\n");
-
-      const detect = await runGSDDoctor(dir);
-      const staleIssues = detect.issues.filter(i => i.code === "stale_uncommitted_changes");
-      assert.deepStrictEqual(staleIssues.length, 0, "recent commit with dirty tree NOT flagged as stale");
-    });
-
-    // ─── Test: stale_uncommitted_changes suppressed by git.snapshots:false (#4420) ──
-    test('stale_uncommitted_changes (suppressed by git.snapshots:false)', async () => {
-      const dir = createRepoWithActiveMilestone();
-      cleanups.push(dir);
-
-      const pastDate = new Date(Date.now() - 45 * 60 * 1000).toISOString();
-      run(`git commit --amend --no-edit --date="${pastDate}"`, dir);
-      execSync(`git commit --amend --no-edit`, {
-        cwd: dir,
-        stdio: ["ignore", "pipe", "pipe"],
-        encoding: "utf-8",
-        env: { ...process.env, GIT_COMMITTER_DATE: pastDate },
-      });
-
-      writeFileSync(join(dir, "README.md"), "# test\nmodified content\n");
-      writeFileSync(join(dir, ".gsd", "PREFERENCES.md"), `---\ngit:\n  snapshots: false\n---\n`);
-
-      const commitsBefore = run("git rev-list --count HEAD", dir);
-
-      const previousCwd = process.cwd();
-      process.chdir(dir);
-      try {
-        const detect = await runGSDDoctor(dir);
-        const staleIssues = detect.issues.filter(i => i.code === "stale_uncommitted_changes");
-        assert.deepStrictEqual(staleIssues.length, 0, "git.snapshots:false suppresses stale detection");
-
-        const fixed = await runGSDDoctor(dir, { fix: true });
-        assert.ok(
-          !fixed.fixesApplied.some(f => f.includes("gsd snapshot")),
-          `git.snapshots:false suppresses snapshot fix (got: ${JSON.stringify(fixed.fixesApplied)})`,
-        );
-      } finally {
-        process.chdir(previousCwd);
-      }
-
-      const commitsAfter = run("git rev-list --count HEAD", dir);
-      assert.strictEqual(commitsAfter, commitsBefore, "no snapshot commit was created when git.snapshots:false");
-    });
-
-    // ─── Test: stale_uncommitted_changes NOT flagged when tree is clean ──
-    test('stale_uncommitted_changes (no false positive on clean tree)', async () => {
-      const dir = createRepoWithActiveMilestone();
-      cleanups.push(dir);
-
-      // Make the last commit appear old
-      const pastDate = new Date(Date.now() - 45 * 60 * 1000).toISOString();
-      run(`git commit --amend --no-edit --date="${pastDate}"`, dir);
-      execSync(`git commit --amend --no-edit`, {
-        cwd: dir,
-        stdio: ["ignore", "pipe", "pipe"],
-        encoding: "utf-8",
-        env: { ...process.env, GIT_COMMITTER_DATE: pastDate },
-      });
-
-      // No uncommitted changes — tree is clean
-      const detect = await runGSDDoctor(dir);
-      const staleIssues = detect.issues.filter(i => i.code === "stale_uncommitted_changes");
-      assert.deepStrictEqual(staleIssues.length, 0, "old commit with clean tree NOT flagged as stale");
-    });
-
-  } finally {
-    for (const dir of cleanups) {
-      try { rmSync(dir, { recursive: true, force: true }); } catch { /* ignore */ }
-    }
-  }
-});