fix(server): storage cleanup treats symlinked spellings of a worktree as one checkout

apps/server/src/storageCleanup.test.ts

@@ -799,6 +799,52 @@ describe("subagent worktree ownership", () => {
     }).pipe(Effect.provide(cleanupTestLayer), Effect.scoped),
   );
 
+  it.effect("keeps a checkout two top-level threads store through a symlinked parent", () =>
+    Effect.gen(function* () {
+      yield* TestClock.setTime(NOW_MS);
+      const fixture = yield* cleanupFixture({
+        ...DEFAULT_SERVER_SETTINGS.storageCleanup,
+        worktreeSettledAfterDays: 8,
+      });
+      const linkedParent = `${yield* fixture.fs.makeTempDirectoryScoped({ prefix: "cleanup-link-" })}/worktrees`;
+      yield* fixture.fs.symlink(fixture.config.worktreesDir, linkedParent);
+      const settled = { branch: "feature", settledAt: at(-20 * DAY_MS) };
+      fixture.setThreads([
+        shell({ ...settled, worktreePath: fixture.worktree }),
+        shell({ ...settled, id: ThreadId.make("other"), worktreePath: `${linkedParent}/feature` }),
+      ]);
+      const report = yield* fixture.service.runNow;
+      expect(report.entries).toEqual([
+        expect.objectContaining({ outcome: "kept", reason: "Shared by 2 threads" }),
+      ]);
+      expect(yield* fixture.fs.exists(fixture.worktree)).toBe(true);
+    }).pipe(Effect.provide(cleanupTestLayer), Effect.scoped),
+  );
+
+  it.effect("keeps a checkout two top-level threads store in different case on Windows", () =>
+    Effect.gen(function* () {
+      yield* TestClock.setTime(NOW_MS);
+      const fixture = yield* cleanupFixture({
+        ...DEFAULT_SERVER_SETTINGS.storageCleanup,
+        worktreeSettledAfterDays: 8,
+      }).pipe(Effect.provideService(HostProcess.Platform, "win32"));
+      const settled = { branch: "feature", settledAt: at(-20 * DAY_MS) };
+      fixture.setThreads([
+        shell({ ...settled, worktreePath: fixture.worktree }),
+        shell({
+          ...settled,
+          id: ThreadId.make("other"),
+          worktreePath: fixture.worktree.toUpperCase(),
+        }),
+      ]);
+      const report = yield* fixture.service.runNow;
+      expect(report.entries).toEqual([
+        expect.objectContaining({ outcome: "kept", reason: "Shared by 2 threads" }),
+      ]);
+      expect(yield* fixture.fs.exists(fixture.worktree)).toBe(true);
+    }).pipe(Effect.provide(cleanupTestLayer), Effect.scoped),
+  );
+
   it.live.each([
     "running",
     "pending",
@@ -1291,18 +1337,30 @@ describe("storage cleanup reports and local file policies", () => {
       }),
     ),
   );
-  it.live.each(["before-check", "while-measuring"] as const)(
-    "keeps a worktree protected by a missing project root (%s)",
-    (timing) =>
+  it.live.each([
+    ["before-check", "stored"],
+    ["while-measuring", "stored"],
+    ["before-check", "symlinked parent"],
+    ["while-measuring", "symlinked parent"],
+  ] as const)(
+    "keeps a worktree protected by a missing project root (%s, %s spelling)",
+    ([timing, spelling]) =>
       runCleanupTest(
         Effect.gen(function* () {
           const fixture = yield* pausedMeasurementFixture();
+          let worktree = fixture.worktree;
+          if (spelling === "symlinked parent") {
+            const linkedParent = `${yield* fixture.fs.makeTempDirectoryScoped({ prefix: "cleanup-link-" })}/worktrees`;
+            yield* fixture.fs.symlink(fixture.config.worktreesDir, linkedParent);
+            worktree = `${linkedParent}/feature`;
+            fixture.setThreads([shell({ branch: "feature", worktreePath: worktree })]);
+          }
           if (timing === "before-check")
-            fixture.setProjectRoots([fixture.repo, `${fixture.worktree}/removed-checkout`]);
+            fixture.setProjectRoots([fixture.repo, `${worktree}/removed-checkout`]);
           const cleanup = yield* fixture.service.runNow.pipe(Effect.forkChild);
           if (timing === "while-measuring") {
             yield* Deferred.await(fixture.measuring);
-            fixture.setProjectRoots([fixture.repo, `${fixture.worktree}/removed-checkout`]);
+            fixture.setProjectRoots([fixture.repo, `${worktree}/removed-checkout`]);
           }
           yield* Deferred.succeed(fixture.resume, undefined);
           const report = yield* Fiber.join(cleanup);
@@ -1533,6 +1591,23 @@ describe("storage cleanup reports and local file policies", () => {
       }),
     ),
   );
+  it.live("keeps a worktree for a live session in a missing folder under its stored alias", () =>
+    runCleanupTest(
+      Effect.gen(function* () {
+        const fixture = yield* cleanupFixture();
+        const linkedParent = `${yield* fixture.fs.makeTempDirectoryScoped({ prefix: "cleanup-link-" })}/worktrees`;
+        yield* fixture.fs.symlink(fixture.config.worktreesDir, linkedParent);
+        fixture.setThreads([shell({ branch: "feature", worktreePath: `${linkedParent}/feature` })]);
+        fixture.setOpenSessionCwd(`${linkedParent}/feature/removed-folder`);
+        const report = yield* fixture.service.runNow;
+        expect(report.entries[0]).toMatchObject({
+          outcome: "kept",
+          reason: "Provider session is still open",
+        });
+        expect(yield* fixture.fs.exists(fixture.worktree)).toBe(true);
+      }),
+    ),
+  );
   it.live("compares the checked-out branch without a full status", () =>
     runCleanupTest(
       Effect.gen(function* () {

apps/server/src/storageCleanup.ts

@@ -240,20 +240,6 @@ const make = Effect.gen(function* () {
       !path.isAbsolute(relative)
     );
   };
-  const hasTerminal = (worktreePath: string) =>
-    [...liveTerminals.values()]
-      .flatMap((entries) => [...entries.values()])
-      .some((terminal) => {
-        if (terminal.status !== "starting" && terminal.status !== "running") return false;
-        const cwd = path.resolve(terminal.cwd);
-        return (
-          (terminal.worktreePath !== null &&
-            path.resolve(terminal.worktreePath) === worktreePath) ||
-          cwd === worktreePath ||
-          inside(worktreePath, cwd)
-        );
-      });
-
   // pnpm imports packages by clone or reflink when its store shares a device
   // with the worktree. Those files have one link but share blocks with the
   // store, so removing them frees almost nothing. A store on another device
@@ -335,18 +321,21 @@ const make = Effect.gen(function* () {
   });
 
   const containsProjectRoot = Effect.fn("StorageCleanup.containsProjectRoot")(function* (
-    worktreePath: string,
+    worktreePaths: ReadonlyArray<string>,
     projects: ReadonlyArray<{ readonly workspaceRoot: string }>,
   ) {
+    const contains = (projectPath: string) =>
+      worktreePaths.some(
+        (worktreePath) =>
+          pathKey(projectPath) === pathKey(worktreePath) || inside(worktreePath, projectPath),
+      );
     for (const project of projects) {
       const projectPath = path.resolve(project.workspaceRoot);
-      if (pathKey(projectPath) === pathKey(worktreePath) || inside(worktreePath, projectPath))
-        return true;
+      if (contains(projectPath)) return true;
       const realPath = yield* fs
         .realPath(projectPath)
         .pipe(Effect.orElseSucceed(() => projectPath));
-      if (pathKey(realPath) === pathKey(worktreePath) || inside(worktreePath, realPath))
-        return true;
+      if (contains(realPath)) return true;
     }
     return false;
   });
@@ -733,13 +722,51 @@ const make = Effect.gen(function* () {
     const snapshot = yield* readThreads();
     const refreshedDefaultRefs = new Map<string, Set<string>>();
     const defaultBranches = new Map<string, string | null>();
-    const groups = Map.groupBy(
-      snapshot.threads.filter((thread) => thread.worktreePath !== null),
-      (thread) => path.resolve(thread.worktreePath!),
+    // Threads may store one checkout through different symlinked spellings; compare real paths.
+    // Keys are only compared, never opened, so they take pathKey's Windows case folding.
+    const canonicalPaths = new Map<string, string>();
+    const canonical = Effect.fnUntraced(function* (target: string) {
+      const resolved = path.resolve(target);
+      const cached = canonicalPaths.get(resolved);
+      if (cached !== undefined) return cached;
+      const realPath = yield* fs.realPath(resolved).pipe(Effect.orElseSucceed(() => resolved));
+      const key = pathKey(realPath);
+      canonicalPaths.set(resolved, key);
+      return key;
+    });
+    // A cwd in a deleted folder cannot be resolved, so stored spellings are compared too.
+    const occupies = Effect.fnUntraced(function* (
+      worktreePaths: ReadonlyArray<string>,
+      target: string,
+    ) {
+      const targets = [path.resolve(target), yield* canonical(target)];
+      return worktreePaths.some((worktree) =>
+        targets.some((cwd) => pathKey(cwd) === pathKey(worktree) || inside(worktree, cwd)),
+      );
+    });
+    const hasTerminal = Effect.fnUntraced(function* (worktreePaths: ReadonlyArray<string>) {
+      for (const terminal of [...liveTerminals.values()].flatMap((entries) => [
+        ...entries.values(),
+      ])) {
+        if (terminal.status !== "starting" && terminal.status !== "running") continue;
+        if (
+          (terminal.worktreePath !== null &&
+            (yield* occupies(worktreePaths, terminal.worktreePath))) ||
+          (yield* occupies(worktreePaths, terminal.cwd))
+        )
+          return true;
+      }
+      return false;
+    });
+    const liveThreads = snapshot.threads.filter((thread) => thread.worktreePath !== null);
+    const liveKeys = yield* Effect.forEach(liveThreads, (thread) =>
+      canonical(thread.worktreePath!),
     );
-    const deletedByPath = Map.groupBy(deletedThreads, (thread) =>
-      path.resolve(thread.worktreePath!),
+    const groups = Map.groupBy(liveThreads, (_thread, index) => liveKeys[index]!);
+    const deletedKeys = yield* Effect.forEach(deletedThreads, (thread) =>
+      canonical(thread.worktreePath!),
     );
+    const deletedByPath = Map.groupBy(deletedThreads, (_thread, index) => deletedKeys[index]!);
     const candidates = [
       ...[...groups].map(
         ([worktreePath, group]) =>
@@ -755,13 +782,15 @@ const make = Effect.gen(function* () {
           worktreeOwner(group) ??
           group[0]!,
       ),
-      ...deletedThreads.filter((thread) => !groups.has(path.resolve(thread.worktreePath!))),
+      ...deletedThreads.filter((_thread, index) => !groups.has(deletedKeys[index]!)),
     ];
     for (const thread of candidates) {
       const settings = resolveWorktreeCleanup(serverSettings, thread.projectId);
       if (!worktreeCleanupEnabled(settings)) continue;
       const worktreePath = path.resolve(thread.worktreePath!);
-      const group = groups.get(worktreePath) ?? [];
+      const worktreeKey = yield* canonical(worktreePath);
+      const worktreePaths = [worktreePath, worktreeKey];
+      const group = groups.get(worktreeKey) ?? [];
       const activityAt = Math.max(...group.map(storageCleanupActivityAt));
       const deleted = "workspaceRoot" in thread;
       const members = deleted ? [thread, ...group] : group;
@@ -793,15 +822,15 @@ const make = Effect.gen(function* () {
           return keep("thread is running or has pending work");
         if (group.some((member) => member.branch !== thread.branch))
           return keep("a subagent thread's branch differs from this worktree's branch");
-        if (hasTerminal(worktreePath)) return keep("open terminal");
+        if (yield* hasTerminal(worktreePaths)) return keep("open terminal");
         // Compare canonical roots while allowing symlinked parents, never symlinked worktree directories.
         const realPath = yield* fs.realPath(worktreePath);
         const realParent = yield* fs.realPath(path.dirname(worktreePath));
         if (realPath !== path.join(realParent, path.basename(worktreePath)))
           return keep("worktree is a symbolic link");
         if (!roots.some((root) => inside(root, realPath)))
           return keep("outside the managed worktree folder");
-        if (yield* containsProjectRoot(worktreePath, [project, ...snapshot.projects]))
+        if (yield* containsProjectRoot(worktreePaths, [project, ...snapshot.projects]))
           return keep("contains a project checkout");
         if ((yield* fs.stat(path.join(worktreePath, ".git"))).type !== "File")
           return keep("not a linked worktree");
@@ -919,12 +948,14 @@ const make = Effect.gen(function* () {
         // Re-read this path's threads and sessions so new activity cancels removal; full per-worktree snapshots take seconds.
         const blockedSinceCheck = Effect.fnUntraced(function* () {
           const latestProjects = yield* projectStore.listShells();
-          if (yield* containsProjectRoot(worktreePath, [project, ...latestProjects]))
+          if (yield* containsProjectRoot(worktreePaths, [project, ...latestProjects]))
             return "contains a project checkout";
-          const latest = (yield* projections.getThreadWorktreePaths({
-            includeArchived: true,
-          })).filter((entry) => path.resolve(entry.worktreePath) === worktreePath);
-          if (hasTerminal(worktreePath)) return "open terminal";
+          const bindings = yield* projections.getThreadWorktreePaths({ includeArchived: true });
+          const bindingKeys = yield* Effect.forEach(bindings, (binding) =>
+            canonical(binding.worktreePath),
+          );
+          const latest = bindings.filter((_binding, index) => bindingKeys[index] === worktreeKey);
+          if (yield* hasTerminal(worktreePaths)) return "open terminal";
           if (deleted) {
             if (
               !resolveWorktreeCleanup(yield* settingsService.getSettings, thread.projectId)
@@ -942,20 +973,23 @@ const make = Effect.gen(function* () {
             projections.getThreadShell(entry.threadId),
           );
           const latestGroup = latestShells.filter((shell) => shell !== null);
+          const latestKeys = yield* Effect.forEach(latestGroup, (shell) =>
+            shell.worktreePath === null ? Effect.succeed(null) : canonical(shell.worktreePath),
+          );
           const latestOwner = worktreeOwner(deleted ? [thread, ...latestGroup] : latestGroup);
           if (
             latestGroup.length !== group.length ||
             latestOwner?.id !== thread.id ||
             latestOwner?.branch !== thread.branch ||
-            latestGroup.some((shell) => {
+            latestGroup.some((shell, index) => {
               const previous = group.find((member) => member.id === shell.id);
               return (
                 previous === undefined ||
                 shell.branch !== thread.branch ||
                 !Equal.equals(shell.settledAt, previous.settledAt) ||
                 (shell.settledAt !== null && !Equal.equals(shell.updatedAt, previous.updatedAt)) ||
                 !storageCleanupThreadIdle(shell, now) ||
-                path.resolve(shell.worktreePath!) !== worktreePath ||
+                latestKeys[index] !== worktreeKey ||
                 storageCleanupActivityAt(shell) !== storageCleanupActivityAt(previous)
               );
             })
@@ -971,9 +1005,8 @@ const make = Effect.gen(function* () {
           );
           // Ready persisted sessions may have released their runtime; only live sessions protect the path.
           for (const session of sessions) {
-            const cwd = path.resolve(session.cwd);
             if (
-              (cwd === worktreePath || inside(worktreePath, cwd)) &&
+              (yield* occupies(worktreePaths, session.cwd)) &&
               (yield* providerSessions.isLive(session.id))
             )
               return "provider session is still open";