diff --git a/packages/storage/src/__tests__/fixtures/git-repository.ts b/packages/storage/src/__tests__/fixtures/git-repository.ts
index 98cacbc201..ad4a9acd03 100644
--- a/packages/storage/src/__tests__/fixtures/git-repository.ts
+++ b/packages/storage/src/__tests__/fixtures/git-repository.ts
@@ -24,6 +24,44 @@ import { promisify } from 'node:util';
 
 const execFileAsync = promisify(execFile);
 
+export const BROKEN_GIT_SHAPES = [
+  'head-directory',
+  'head-garbage',
+  'head-symref-no-refs-prefix',
+  'gitfile-garbage-head',
+  'missing-objects-and-refs',
+] as const;
+
+export type BrokenGitShape = (typeof BROKEN_GIT_SHAPES)[number];
+
+/** Writes structurally broken Git metadata (a `.git` entry or its target) into root. */
+export async function createBrokenGitMetadata(root: string, shape: BrokenGitShape): Promise<void> {
+  switch (shape) {
+    case 'head-directory':
+      await mkdir(join(root, '.git', 'HEAD'), { recursive: true });
+      return;
+    case 'head-garbage':
+      await mkdir(join(root, '.git'), { recursive: true });
+      await writeFile(join(root, '.git', 'HEAD'), 'gk\n', 'utf8');
+      return;
+    case 'gitfile-garbage-head':
+      await writeFile(join(root, '.git'), 'gitdir: stub\n', 'utf8');
+      await mkdir(join(root, 'stub'), { recursive: true });
+      await writeFile(join(root, 'stub', 'HEAD'), 'gk\n', 'utf8');
+      return;
+    case 'head-symref-no-refs-prefix':
+      // Valid objects/ and refs/ plus a symref whose target is not under
+      // refs/: passes naive checks but git rev-parse exits 128.
+      await mkdir(join(root, '.git', 'objects'), { recursive: true });
+      await mkdir(join(root, '.git', 'refs'), { recursive: true });
+      await writeFile(join(root, '.git', 'HEAD'), 'ref: gk\n', 'utf8');
+      return;
+    case 'missing-objects-and-refs':
+      await mkdir(join(root, '.git'), { recursive: true });
+      await writeFile(join(root, '.git', 'HEAD'), `ref: refs/heads/${'a'.repeat(40)}\n`, 'utf8');
+  }
+}
+
 export async function createGitRepositoryWithWorktree(
   repository: string,
   linkedWorktree: string,
diff --git a/packages/storage/src/__tests__/project-catalog.test.ts b/packages/storage/src/__tests__/project-catalog.test.ts
index 6348662534..89fceca823 100644
--- a/packages/storage/src/__tests__/project-catalog.test.ts
+++ b/packages/storage/src/__tests__/project-catalog.test.ts
@@ -35,7 +35,11 @@ import {
   resolveProjectLocation,
 } from '../project-catalog.js';
 import { createSessionStore } from '../session-store.js';
-import { createGitRepositoryWithWorktree } from './fixtures/git-repository.js';
+import {
+  BROKEN_GIT_SHAPES,
+  createBrokenGitMetadata,
+  createGitRepositoryWithWorktree,
+} from './fixtures/git-repository.js';
 
 const execFileAsync = promisify(execFile);
 const trackedCatalogs = new Map<ProjectCatalog, string>();
@@ -99,6 +103,82 @@ test('a plain folder resolves without requiring the Git executable', async () =>
   }
 });
 
+test('an incomplete enclosing .git directory does not turn a nested folder into a repository', async () => {
+  const base = await mkdtemp(join(tmpdir(), 'maka-project-folder-invalid-git-'));
+  try {
+    const folder = join(base, 'folder');
+    await mkdir(join(base, '.git', 'gk'), { recursive: true });
+    await mkdir(folder);
+
+    assert.deepEqual(await resolveProjectLocationWithoutGit(folder), {
+      canonicalPath: await realpath(folder),
+      identity: `folder:${await realpath(folder)}`,
+      kind: 'folder',
+    });
+  } finally {
+    await rm(base, { recursive: true, force: true });
+  }
+});
+
+test('broken ancestor Git metadata does not turn a nested folder into a repository', async () => {
+  const base = await mkdtemp(join(tmpdir(), 'maka-project-invalid-ancestor-'));
+  try {
+    for (const shape of BROKEN_GIT_SHAPES) {
+      const root = join(base, shape);
+      const folder = join(root, 'folder');
+      await mkdir(folder, { recursive: true });
+      await createBrokenGitMetadata(root, shape);
+
+      assert.deepEqual(
+        await resolveProjectLocation({ path: folder }),
+        {
+          canonicalPath: await realpath(folder),
+          identity: `folder:${await realpath(folder)}`,
+          kind: 'folder',
+        },
+        shape,
+      );
+    }
+  } finally {
+    await rm(base, { recursive: true, force: true });
+  }
+});
+
+test('a folder nested inside a repository resolves to that repository', async () => {
+  const base = await mkdtemp(join(tmpdir(), 'maka-project-nested-in-repo-'));
+  try {
+    const repository = join(base, 'repository');
+    const nested = join(repository, 'sub', 'dir');
+    await mkdir(nested, { recursive: true });
+    await execFileAsync('git', ['init', '--quiet'], { cwd: repository });
+
+    const resolved = await resolveProjectLocation({ path: nested });
+
+    assert.equal(resolved.kind, 'git');
+    assert.equal(resolved.git?.worktreeRoot, await realpath(repository));
+  } finally {
+    await rm(base, { recursive: true, force: true });
+  }
+});
+
+test('a folder nested inside a linked worktree resolves to that repository', async () => {
+  const base = await mkdtemp(join(tmpdir(), 'maka-project-nested-in-worktree-'));
+  try {
+    const repository = join(base, 'repository');
+    const linkedWorktree = join(base, 'linked');
+    await createGitRepositoryWithWorktree(repository, linkedWorktree, 'nested-linked');
+    const nested = join(linkedWorktree, 'nested');
+    await mkdir(nested);
+
+    const resolved = await resolveProjectLocation({ path: nested });
+
+    assert.equal(resolved.kind, 'git');
+    assert.equal(resolved.git?.isWorktree, true);
+  } finally {
+    await rm(base, { recursive: true, force: true });
+  }
+});
+
 test('a Git probe failure cannot persistently downgrade a repository to a folder', async () => {
   const base = await mkdtemp(join(tmpdir(), 'maka-project-repository-no-git-'));
   try {
diff --git a/packages/storage/src/__tests__/workspace-identity.test.ts b/packages/storage/src/__tests__/workspace-identity.test.ts
index 22ed636cff..8dd73a288f 100644
--- a/packages/storage/src/__tests__/workspace-identity.test.ts
+++ b/packages/storage/src/__tests__/workspace-identity.test.ts
@@ -19,7 +19,7 @@
 
 import assert from 'node:assert/strict';
 import { execFile } from 'node:child_process';
-import { access, chmod, mkdir, mkdtemp, readFile, rm, writeFile } from 'node:fs/promises';
+import { access, chmod, mkdir, mkdtemp, readFile, rm, symlink, writeFile } from 'node:fs/promises';
 import { tmpdir } from 'node:os';
 import { join } from 'node:path';
 import { test } from 'node:test';
@@ -31,6 +31,7 @@ import {
   WORKSPACE_MARKER_FILE,
   WorkspaceIdentityError,
 } from '../workspace-identity.js';
+import { BROKEN_GIT_SHAPES, createBrokenGitMetadata } from './fixtures/git-repository.js';
 
 const execFileAsync = promisify(execFile);
 
@@ -200,6 +201,38 @@ test('a full Git exclude does not grow when resolving workspace identity', async
   }
 });
 
+test('a malformed ancestor .git directory does not block a workspace marker', async () => {
+  const base = await mkdtemp(join(tmpdir(), 'maka-workspace-git-malformed-ancestor-'));
+  try {
+    const workspace = join(base, 'workspace');
+    await mkdir(join(base, '.git', 'gk'), { recursive: true });
+    await mkdir(workspace);
+
+    await resolveWorkspaceIdentityWithoutGit(workspace);
+
+    await access(join(workspace, WORKSPACE_MARKER_FILE));
+  } finally {
+    await rm(base, { recursive: true, force: true });
+  }
+});
+
+test('broken ancestor Git metadata does not block a workspace marker', async () => {
+  const base = await mkdtemp(join(tmpdir(), 'maka-workspace-invalid-ancestor-'));
+  try {
+    for (const shape of BROKEN_GIT_SHAPES) {
+      const root = join(base, shape);
+      const workspace = join(root, 'workspace');
+      await mkdir(workspace, { recursive: true });
+      await createBrokenGitMetadata(root, shape);
+
+      await resolveWorkspaceIdentity({ path: workspace });
+      await access(join(workspace, WORKSPACE_MARKER_FILE));
+    }
+  } finally {
+    await rm(base, { recursive: true, force: true });
+  }
+});
+
 test('a malformed enclosing Git repository prevents publishing a new marker', async () => {
   const workspace = await mkdtemp(join(tmpdir(), 'maka-workspace-git-malformed-'));
   try {
@@ -216,6 +249,27 @@ test('a malformed enclosing Git repository prevents publishing a new marker', as
   }
 });
 
+test('a dangling .git symlink in the workspace itself blocks marker publication', {
+  skip:
+    process.platform === 'win32'
+      ? 'Windows symlink creation requires elevated privileges or Developer Mode'
+      : false,
+}, async () => {
+  const workspace = await mkdtemp(join(tmpdir(), 'maka-workspace-git-dangling-'));
+  try {
+    await symlink(join(workspace, 'missing-target'), join(workspace, '.git'));
+
+    await assert.rejects(
+      () => resolveWorkspaceIdentity({ path: workspace }),
+      (error: unknown) =>
+        error instanceof WorkspaceIdentityError && error.code === 'workspace_io_failed',
+    );
+    await assert.rejects(access(join(workspace, WORKSPACE_MARKER_FILE)), { code: 'ENOENT' });
+  } finally {
+    await rm(workspace, { recursive: true, force: true });
+  }
+});
+
 test('a non-Git workspace resolves when the Git executable is unavailable', async () => {
   const workspace = await mkdtemp(join(tmpdir(), 'maka-workspace-no-git-required-'));
   try {
diff --git a/packages/storage/src/git-entry.ts b/packages/storage/src/git-entry.ts
index db998487b6..9e179bd71f 100644
--- a/packages/storage/src/git-entry.ts
+++ b/packages/storage/src/git-entry.ts
@@ -17,21 +17,86 @@
  * under the License.
  */
 
-import { lstat } from 'node:fs/promises';
-import { join, parse } from 'node:path';
+import { lstat, readFile, stat } from 'node:fs/promises';
+import { join, parse, resolve } from 'node:path';
+
+const GITDIR_PREFIX = 'gitdir: ';
+const HEAD_REF_PREFIX = 'ref: ';
+// HEAD holds a 40-char SHA-1 object id, or 64 chars for SHA-256 repositories.
+const HEAD_OBJECT_ID = /^[0-9a-f]{40}(?:[0-9a-f]{24})?$/;
 
 export async function hasEnclosingGitEntry(path: string): Promise<boolean> {
   let current = path;
   while (true) {
+    const gitPath = join(current, '.git');
     try {
-      await lstat(join(current, '.git'));
-      return true;
+      // lstat does not follow symlinks, so a dangling `.git` symlink still
+      // counts as an existing entry. The selected directory fails closed
+      // downstream when its own Git metadata is damaged; an ancestor only
+      // counts when it is structurally valid.
+      const entry = await lstat(gitPath);
+      if (current === path) return true;
+      const gitStat = entry.isSymbolicLink() ? await stat(gitPath) : entry;
+      if (gitStat.isDirectory()) return isGitDirectory(gitPath);
+      if (gitStat.isFile()) {
+        const content = (await readFile(gitPath, 'utf8')).trim();
+        if (!content.startsWith(GITDIR_PREFIX)) return false;
+        const target = content.slice(GITDIR_PREFIX.length).trim();
+        if (!target) return false;
+        return isGitDirectory(resolve(current, target));
+      }
+      return false;
     } catch (error) {
       const code = (error as NodeJS.ErrnoException).code;
-      if (code !== 'ENOENT' && code !== 'ENOTDIR') throw error;
+      if (code !== 'ENOENT' && code !== 'ENOTDIR') return current === path;
     }
     const parent = parse(current).dir;
     if (parent === current) return false;
     current = parent;
   }
 }
+
+/**
+ * Checks the minimum Git directory contract git-rev-parse relies on: a
+ * readable regular HEAD holding either a symref or an object id, plus the
+ * objects and refs directories. Anything else would make the downstream Git
+ * commands fail closed instead of being treated as an enclosing repository.
+ */
+async function isGitDirectory(gitDir: string): Promise<boolean> {
+  try {
+    // readFile fails closed on a missing, unreadable, or directory HEAD.
+    const head = (await readFile(join(gitDir, 'HEAD'), 'utf8')).trim();
+    // A symref must target a ref under refs/; git itself rejects any other
+    // target (e.g. `ref: gk`) with exit 128 even when objects/ and refs/ exist.
+    const validHead = head.startsWith(HEAD_REF_PREFIX)
+      ? head.slice(HEAD_REF_PREFIX.length).trim().startsWith('refs/')
+      : HEAD_OBJECT_ID.test(head);
+    if (!validHead) return false;
+  } catch {
+    return false;
+  }
+  // Linked worktrees keep HEAD locally but share objects/refs with the
+  // common dir named by their commondir file.
+  return (
+    (await hasGitSubdirectory(gitDir, 'objects')) && (await hasGitSubdirectory(gitDir, 'refs'))
+  );
+}
+
+async function hasGitSubdirectory(gitDir: string, name: string): Promise<boolean> {
+  if (await isDirectory(join(gitDir, name))) return true;
+  try {
+    const commonDir = (await readFile(join(gitDir, 'commondir'), 'utf8')).trim();
+    return commonDir !== '' && (await isDirectory(resolve(gitDir, commonDir, name)));
+  } catch {
+    // No commondir file: a plain Git directory.
+    return false;
+  }
+}
+
+async function isDirectory(path: string): Promise<boolean> {
+  try {
+    return (await stat(path)).isDirectory();
+  } catch {
+    return false;
+  }
+}