diff --git a/gitnexus/src/cli/clean.ts b/gitnexus/src/cli/clean.ts
index b7c810a7c..51b57db23 100644
--- a/gitnexus/src/cli/clean.ts
+++ b/gitnexus/src/cli/clean.ts
@@ -33,6 +33,13 @@ import {
   listParkedLbugSidecars,
 } from '../core/lbug/sidecar-recovery.js';
 import { t } from './i18n/index.js';
+import { getGlobalDir } from '../storage/global-dir.js';
+import { STORES_DIR } from '../storage/shared-store.js';
+import {
+  reclaimAfterSlotRemoval,
+  reclaimSharedStore,
+  type ReclaimResult,
+} from '../storage/shared-store-lifecycle.js';
 
 type OwnedCwdStorage = {
   repo: NonNullable<Awaited<ReturnType<typeof findRepo>>>;
@@ -147,13 +154,50 @@ const cleanStaleBranchSlots = async (force: boolean): Promise<void> => {
   }
 };
 
+const reportReclaim = (result: ReclaimResult | null): void => {
+  if (!result) return;
+  if (result.removed.length > 0) {
+    console.log(t('clean.shared.reclaimed', { count: result.removed.length }));
+  }
+  if (result.kept.length > 0) console.log(t('clean.shared.kept', { count: result.kept.length }));
+};
+
+/** `clean --gc`: collect every shared store under GITNEXUS_HOME (#3352). */
+const collectSharedStores = async (): Promise<void> => {
+  const storesDir = path.join(getGlobalDir(), STORES_DIR);
+  const names = await fs.readdir(storesDir).catch(() => [] as string[]);
+  if (names.length === 0) {
+    console.log(t('clean.gc.none'));
+    return;
+  }
+  for (const name of names) {
+    const root = path.join(storesDir, name);
+    const result = await reclaimSharedStore(root, { gc: true });
+    console.log(
+      t('clean.gc.store', {
+        path: root,
+        members: result.droppedMembers.length,
+        graphs: result.removed.length,
+      }),
+    );
+    if (result.kept.length > 0) console.log(t('clean.shared.kept', { count: result.kept.length }));
+    if (result.storeRemoved) console.log(t('clean.shared.storeRemoved', { path: root }));
+  }
+};
+
 export const cleanCommand = async (options?: {
   force?: boolean;
   all?: boolean;
   lbugSidecars?: boolean;
   stale?: boolean;
   branch?: string;
+  gc?: boolean;
 }) => {
+  if (options?.gc) {
+    await collectSharedStores();
+    return;
+  }
+
   // --stale: reclaim leftover per-branch slots whose recorded branch is not
   // a live local head (#3331). Exclusive arm before --branch.
   if (options?.stale) {
@@ -295,6 +339,7 @@ export const cleanCommand = async (options?: {
         await fs.rm(storagePath, { recursive: true, force: true });
         await unregisterRepo(entry.path);
         console.log(t('clean.deletedRepo', { name: entry.name, storagePath }));
+        reportReclaim(await reclaimAfterSlotRemoval(storagePath));
       } catch (err) {
         if (err instanceof StorageDeletionError) {
           logger.error(`Refusing to clean ${entry.name}: ${err.message}`);
@@ -341,6 +386,7 @@ export const cleanCommand = async (options?: {
     await fs.rm(storagePath, { recursive: true, force: true });
     await unregisterRepo(repo.repoPath);
     console.log(t('common.deleted', { target: storagePath }));
+    reportReclaim(await reclaimAfterSlotRemoval(storagePath));
   } catch (err) {
     logger.error({ err }, 'Failed to delete:');
   }
diff --git a/gitnexus/src/cli/i18n/en.ts b/gitnexus/src/cli/i18n/en.ts
index 932d36b25..ea08053ce 100644
--- a/gitnexus/src/cli/i18n/en.ts
+++ b/gitnexus/src/cli/i18n/en.ts
@@ -59,6 +59,14 @@ export const en = {
   'clean.deleteAll': 'This will delete GitNexus indexes for {{count}} repo(s):',
   'clean.deletedRepo': 'Deleted: {{name}} ({{storagePath}})',
   'clean.notFoundHere': 'No indexed repository found in this directory.',
+  'clean.shared.reclaimed':
+    'Shared store: removed {{count}} commit graph(s) no checkout references.',
+  'clean.shared.kept':
+    'Shared store: kept {{count}} unreferenced commit graph(s) that are still open; run `gitnexus clean --gc` later.',
+  'clean.shared.storeRemoved': 'Shared store: removed {{path}} (no checkouts remain).',
+  'clean.gc.none': 'No shared stores to collect.',
+  'clean.gc.store':
+    'Shared store {{path}}: dropped {{members}} checkout(s), removed {{graphs}} commit graph(s).',
   'clean.deleteCurrent': 'This will delete the GitNexus index for: {{repoName}}',
   'clean.branchNotIndexed':
     'No indexed branch named "{{branch}}" for this repository. Use `gitnexus clean --stale` to reclaim leftover branch indexes, or `gitnexus list` to see recorded names.',
diff --git a/gitnexus/src/cli/i18n/zh-CN.ts b/gitnexus/src/cli/i18n/zh-CN.ts
index 5fde76516..c18f106e7 100644
--- a/gitnexus/src/cli/i18n/zh-CN.ts
+++ b/gitnexus/src/cli/i18n/zh-CN.ts
@@ -58,6 +58,12 @@ export const zhCN = {
   'clean.deleteAll': '将删除 {{count}} 个仓库的 GitNexus 索引：',
   'clean.deletedRepo': '已删除：{{name}}（{{storagePath}}）',
   'clean.notFoundHere': '当前目录未找到已索引仓库。',
+  'clean.shared.reclaimed': '共享存储：已删除 {{count}} 个不再被任何检出引用的提交图。',
+  'clean.shared.kept':
+    '共享存储：保留了 {{count}} 个仍处于打开状态的未引用提交图；请稍后运行 `gitnexus clean --gc`。',
+  'clean.shared.storeRemoved': '共享存储：已删除 {{path}}（没有剩余检出）。',
+  'clean.gc.none': '没有可回收的共享存储。',
+  'clean.gc.store': '共享存储 {{path}}：移除了 {{members}} 个检出，删除了 {{graphs}} 个提交图。',
   'clean.deleteCurrent': '将删除该仓库的 GitNexus 索引：{{repoName}}',
   'clean.branchNotIndexed':
     '该仓库没有名为 “{{branch}}” 的已索引分支。使用 `gitnexus clean --stale` 回收残留分支索引，或使用 `gitnexus list` 查看已记录名称。',
diff --git a/gitnexus/src/cli/index.ts b/gitnexus/src/cli/index.ts
index 01e7be835..897c03764 100644
--- a/gitnexus/src/cli/index.ts
+++ b/gitnexus/src/cli/index.ts
@@ -350,6 +350,10 @@ program
   .option('--all', 'Clean all indexed repos')
   .option('--branch <name>', 'Delete only the named branch index (not the workspace index)')
   .option('--stale', 'Reclaim leftover branch indexes that are not a live local head')
+  .option(
+    '--gc',
+    'Drop shared-store checkouts whose worktree is gone and delete commit graphs nothing references',
+  )
   .option(
     '--lbug-sidecars',
     'Clean parked LadybugDB recovery sidecars (missing-shadow WAL quarantines and dirty-recovery parks)',
diff --git a/gitnexus/src/cli/remove.ts b/gitnexus/src/cli/remove.ts
index 72bb92364..697200a62 100644
--- a/gitnexus/src/cli/remove.ts
+++ b/gitnexus/src/cli/remove.ts
@@ -29,6 +29,7 @@
  *     here there is no pipeline, so no conflation.)
  */
 
+import { reclaimAfterSlotRemoval } from '../storage/shared-store-lifecycle.js';
 import fs from 'fs/promises';
 import { logger } from '../core/logger.js';
 import { cliError } from './cli-message.js';
@@ -100,6 +101,7 @@ export const removeCommand = async (target: string, options?: { force?: boolean
   try {
     await fs.rm(storagePath, { recursive: true, force: true });
     await unregisterRepo(entry.path);
+    await reclaimAfterSlotRemoval(storagePath);
     console.log(t('remove.removed', { name: entry.name }));
     console.log(`   ${t('common.path')}:    ${entry.path}`);
     console.log(`   ${t('common.storage')}: ${entry.storagePath}`);
diff --git a/gitnexus/src/core/shared-store-analyze.ts b/gitnexus/src/core/shared-store-analyze.ts
index e6167caaa..c969323ad 100644
--- a/gitnexus/src/core/shared-store-analyze.ts
+++ b/gitnexus/src/core/shared-store-analyze.ts
@@ -19,7 +19,8 @@ import { createHash, randomUUID } from 'crypto';
 import { constants as fsConstants } from 'fs';
 import fs from 'fs/promises';
 import path from 'path';
-import { acquireIndexLock, requireExclusiveIndexLock } from '../storage/index-lock.js';
+import { acquireIndexLock } from '../storage/index-lock.js';
+import { withStoreLock } from '../storage/shared-store-lifecycle.js';
 import { commitDistanceToHead, isWorkingTreeDirty } from '../storage/git.js';
 import { registerRepo, saveMeta } from '../storage/repo-manager.js';
 import { loadMeta, type RepoMeta } from '../storage/repo-meta.js';
@@ -250,26 +251,6 @@ export const ensurePrivateSharedGraph = async (slot: string, log: Log): Promise<
   return true;
 };
 
-/**
- * Serialize one kind of store-wide write (`publish`, `cache`) across
- * checkouts. Each checkout's own slot is already covered by its index lock.
- */
-export const withStoreLock = async <T>(
-  layout: SharedStoreLayout,
-  name: 'publish' | 'cache',
-  fn: () => Promise<T>,
-): Promise<T> => {
-  const lockDir = path.join(layout.root, 'locks', name);
-  await fs.mkdir(lockDir, { recursive: true });
-  const lock = await acquireIndexLock(lockDir);
-  try {
-    requireExclusiveIndexLock(lock, `Cannot acquire the shared-store ${name} lock at ${lockDir}.`);
-    return await fn();
-  } finally {
-    lock.release();
-  }
-};
-
 /**
  * Every directory in the store whose metadata may record parse-cache keys:
  * each checkout slot (its branch slots are read by the caller's per-root
@@ -350,3 +331,5 @@ export const publishSharedGraph = async (
   // must still end up registered at its slot.
   await registerRepo(repoPath, meta, { storagePath: slot });
 };
+
+export { withStoreLock };
diff --git a/gitnexus/src/server/api.ts b/gitnexus/src/server/api.ts
index d10a4fd47..70c23fa80 100644
--- a/gitnexus/src/server/api.ts
+++ b/gitnexus/src/server/api.ts
@@ -8,6 +8,7 @@
  * CORS is restricted to localhost, private/LAN networks, and the deployed site.
  */
 
+import { reclaimAfterSlotRemoval } from '../storage/shared-store-lifecycle.js';
 import express from 'express';
 import cors from 'cors';
 import path from 'path';
@@ -1318,6 +1319,7 @@ export const createServer = async (port: number, host: string = '127.0.0.1') =>
 
         // 1. Delete the .gitnexus index/storage directory
         await fs.rm(storagePath, { recursive: true, force: true }).catch(() => {});
+        await reclaimAfterSlotRemoval(storagePath);
 
         // 2. Delete the cloned repo dir if it lives under ~/.gitnexus/repos/.
         // getCloneDir now throws on names that are not filesystem-safe (e.g.
diff --git a/gitnexus/src/storage/shared-store-lifecycle.ts b/gitnexus/src/storage/shared-store-lifecycle.ts
new file mode 100644
index 000000000..c0d8c6131
--- /dev/null
+++ b/gitnexus/src/storage/shared-store-lifecycle.ts
@@ -0,0 +1,157 @@
+/**
+ * Store-wide locking and reference-counted cleanup for the shared sibling
+ * store (#3352).
+ *
+ * A commit graph is live while any member checkout slot's metadata records
+ * it as `graphPath`. `reclaimSharedStore` deletes every commit graph with no
+ * reference, and the whole store once no member and no commit graph remain.
+ * It runs under the store's publish lock, so a concurrent analyze that is
+ * publishing or pointing at a graph is never raced.
+ */
+
+import { existsSync } from 'fs';
+import fs from 'fs/promises';
+import path from 'path';
+import { acquireIndexLock, requireExclusiveIndexLock } from './index-lock.js';
+import { loadMeta } from './repo-meta.js';
+import {
+  resolveSharedStore,
+  storeRootOfCheckoutSlot,
+  type SharedStoreLayout,
+} from './shared-store.js';
+import { LBUG_DIRECTORY } from './storage-constants.js';
+
+type StoreRoot = Pick<SharedStoreLayout, 'root'>;
+
+/**
+ * Serialize one kind of store-wide write (`publish`, `cache`) across
+ * checkouts. Each checkout's own slot is already covered by its index lock.
+ */
+export const withStoreLock = async <T>(
+  layout: StoreRoot,
+  name: 'publish' | 'cache',
+  fn: () => Promise<T>,
+): Promise<T> => {
+  const lockDir = path.join(layout.root, 'locks', name);
+  await fs.mkdir(lockDir, { recursive: true });
+  const lock = await acquireIndexLock(lockDir);
+  try {
+    requireExclusiveIndexLock(lock, `Cannot acquire the shared-store ${name} lock at ${lockDir}.`);
+    return await fn();
+  } finally {
+    lock.release();
+  }
+};
+
+export interface ReclaimResult {
+  /** Commit graph directories deleted. */
+  removed: string[];
+  /** Unreferenced commit graphs that could not be deleted (for example, open on Windows). */
+  kept: string[];
+  /** Member slots dropped by garbage collection. */
+  droppedMembers: string[];
+  /** The store root was deleted because nothing remained. */
+  storeRemoved: boolean;
+}
+
+const listDir = (dir: string): Promise<string[]> => fs.readdir(dir).catch(() => [] as string[]);
+
+/**
+ * A member slot whose checkout is gone or no longer resolves to this store
+ * (the worktree was deleted, or sharing was turned off for it).
+ */
+const isOrphanMember = async (slot: string, storeRoot: string): Promise<boolean> => {
+  const meta = await loadMeta(slot);
+  if (!meta?.repoPath) return false; // unknown slot: never collect what we cannot attribute
+  if (!existsSync(meta.repoPath)) return true;
+  const layout = resolveSharedStore(meta.repoPath);
+  return !layout || layout.root !== storeRoot || layout.checkoutSlot !== slot;
+};
+
+/**
+ * Delete unreferenced commit graphs, stale publish staging, and — with `gc` —
+ * member slots whose checkout no longer belongs to the store. Removes the
+ * store itself when nothing remains.
+ */
+export const reclaimSharedStore = async (
+  storeRoot: string,
+  opts: { gc?: boolean } = {},
+): Promise<ReclaimResult> => {
+  const result: ReclaimResult = { removed: [], kept: [], droppedMembers: [], storeRemoved: false };
+  if (!existsSync(storeRoot)) return result;
+  const checkoutsDir = path.join(storeRoot, 'checkouts');
+  const commitsDir = path.join(storeRoot, 'commits');
+
+  await withStoreLock({ root: storeRoot }, 'publish', async () => {
+    const referenced = new Set<string>();
+    let slots = (await listDir(checkoutsDir)).map((name) => path.join(checkoutsDir, name));
+    if (opts.gc) {
+      const live: string[] = [];
+      for (const slot of slots) {
+        if (await isOrphanMember(slot, storeRoot)) {
+          await fs.rm(slot, { recursive: true, force: true });
+          result.droppedMembers.push(slot);
+        } else {
+          live.push(slot);
+        }
+      }
+      slots = live;
+    }
+    for (const slot of slots) {
+      const graphPath = (await loadMeta(slot))?.graphPath;
+      if (graphPath) referenced.add(path.dirname(path.resolve(graphPath)));
+    }
+
+    for (const name of await listDir(commitsDir)) {
+      const dir = path.join(commitsDir, name);
+      if (referenced.has(dir)) continue;
+      try {
+        await fs.rm(dir, { recursive: true, force: true });
+        if (!name.startsWith('.')) result.removed.push(dir);
+      } catch {
+        // Windows refuses to delete a file another process has open (an MCP
+        // reader). Keep it for the next reclaim instead of failing the clean.
+        if (!name.startsWith('.')) result.kept.push(dir);
+      }
+    }
+
+    const remaining = (await listDir(checkoutsDir)).length + (await listDir(commitsDir)).length;
+    if (remaining === 0) {
+      // The lock directory lives inside the store; removing it while held is
+      // safe on POSIX and is retried on the next reclaim elsewhere.
+      await fs
+        .rm(storeRoot, { recursive: true, force: true })
+        .then(() => {
+          result.storeRemoved = true;
+        })
+        .catch(() => {});
+    }
+  });
+  return result;
+};
+
+/**
+ * After a storage slot was deleted: reclaim its store when it was a shared
+ * checkout slot. No-op for any other storage path. Never throws — the slot
+ * deletion already succeeded and reclaim is retried by the next clean.
+ */
+export const reclaimAfterSlotRemoval = async (
+  storagePath: string,
+): Promise<ReclaimResult | null> => {
+  const storeRoot = storeRootOfCheckoutSlot(storagePath);
+  if (!storeRoot) return null;
+  try {
+    return await reclaimSharedStore(storeRoot);
+  } catch {
+    return null;
+  }
+};
+
+/** Graph directory a checkout slot reads, for reporting. */
+export const describeSharedGraph = (
+  graphPath: string,
+  storagePath: string,
+): 'shared' | 'private' =>
+  path.resolve(graphPath) === path.join(path.resolve(storagePath), LBUG_DIRECTORY)
+    ? 'private'
+    : 'shared';
diff --git a/gitnexus/test/integration/shared-store-clean.test.ts b/gitnexus/test/integration/shared-store-clean.test.ts
new file mode 100644
index 000000000..cae8f59ac
--- /dev/null
+++ b/gitnexus/test/integration/shared-store-clean.test.ts
@@ -0,0 +1,221 @@
+import { execFileSync } from 'child_process';
+import { existsSync } from 'fs';
+import fs from 'fs/promises';
+import path from 'path';
+import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest';
+import { getStoragePaths, loadMeta, saveMeta } from '../../src/storage/repo-manager.js';
+import {
+  resolveSharedStore,
+  sharedStoreLayout,
+  type SharedStoreLayout,
+} from '../../src/storage/shared-store.js';
+import {
+  reclaimAfterSlotRemoval,
+  reclaimSharedStore,
+} from '../../src/storage/shared-store-lifecycle.js';
+import { createTempDir } from '../helpers/test-db.js';
+
+/**
+ * #3352 U6 — clean removes only what no remaining member references.
+ */
+const git = (cwd: string, ...args: string[]): string =>
+  execFileSync('git', args, { cwd, stdio: 'pipe', encoding: 'utf-8' }).trim();
+
+const commitAll = (cwd: string, message: string): void => {
+  git(cwd, 'add', '-A');
+  git(cwd, '-c', 'user.name=t', '-c', 'user.email=t@t', 'commit', '-q', '-m', message);
+};
+
+const layoutOf = (checkout: string): SharedStoreLayout => {
+  const layout = resolveSharedStore(checkout);
+  expect(layout).not.toBeNull();
+  return layout as SharedStoreLayout;
+};
+
+const commitDirs = async (layout: SharedStoreLayout): Promise<string[]> =>
+  (await fs.readdir(layout.commitsDir).catch(() => [] as string[])).filter(
+    (n) => !n.startsWith('.'),
+  );
+
+describe('shared store clean (#3352)', () => {
+  let tmpHome: Awaited<ReturnType<typeof createTempDir>>;
+  let tmpRepo: Awaited<ReturnType<typeof createTempDir>>;
+  let savedHome: string | undefined;
+  let savedCwd: string;
+  let main: string;
+  let wtA: string;
+  let wtB: string;
+
+  const analyze = async (checkout: string) => {
+    const { runFullAnalysis } = await import('../../src/core/run-analyze.js');
+    return runFullAnalysis(checkout, {}, { onProgress: () => {} });
+  };
+
+  const cleanIn = async (checkout: string, options: Record<string, unknown>) => {
+    const { cleanCommand } = await import('../../src/cli/clean.js');
+    process.chdir(checkout);
+    const log = vi.spyOn(console, 'log').mockImplementation(() => {});
+    try {
+      await cleanCommand(options);
+      return log.mock.calls.map((c) => String(c[0]));
+    } finally {
+      log.mockRestore();
+      process.chdir(savedCwd);
+    }
+  };
+
+  beforeEach(async () => {
+    savedCwd = process.cwd();
+    tmpHome = await createTempDir('gitnexus-clean-home-');
+    tmpRepo = await createTempDir('gitnexus-clean-repo-');
+    savedHome = process.env.GITNEXUS_HOME;
+    process.env.GITNEXUS_HOME = tmpHome.dbPath;
+    const root = await fs.realpath(tmpRepo.dbPath);
+    main = path.join(root, 'main');
+    await fs.mkdir(main);
+    git(main, 'init', '-q', '-b', 'main');
+    await fs.writeFile(path.join(main, 'a.ts'), 'export function alpha() { return 1; }\n');
+    commitAll(main, 'init');
+    wtA = path.join(root, 'wt-a');
+    wtB = path.join(root, 'wt-b');
+    git(main, 'worktree', 'add', '-q', '-b', 'wt-a', wtA);
+    git(main, 'worktree', 'add', '-q', '-b', 'wt-b', wtB);
+  });
+
+  afterEach(async () => {
+    process.chdir(savedCwd);
+    if (savedHome === undefined) delete process.env.GITNEXUS_HOME;
+    else process.env.GITNEXUS_HOME = savedHome;
+    await tmpRepo.cleanup();
+    await tmpHome.cleanup();
+  });
+
+  it('Covers AE5: cleaning one of two worktrees at X keeps X for the other', async () => {
+    await analyze(wtA);
+    await analyze(wtB);
+    const graph = getStoragePaths(wtB, undefined, layoutOf(wtB).checkoutSlot).lbugPath;
+
+    await cleanIn(wtA, { force: true });
+
+    expect(existsSync(layoutOf(wtA).checkoutSlot)).toBe(false);
+    expect(existsSync(graph)).toBe(true);
+    expect((await loadMeta(layoutOf(wtB).checkoutSlot))?.graphPath).toBe(graph);
+  }, 240_000);
+
+  it('deletes the commit graph and the store when the last member is cleaned', async () => {
+    await analyze(wtA);
+    await analyze(wtB);
+    const layout = layoutOf(wtA);
+
+    await cleanIn(wtA, { force: true });
+    const logs = await cleanIn(wtB, { force: true });
+
+    expect(await commitDirs(layout)).toEqual([]);
+    expect(existsSync(layout.root)).toBe(false);
+    expect(logs.join('\n')).toMatch(/removed 1 commit graph/);
+  }, 240_000);
+
+  it('previews without --force and deletes nothing', async () => {
+    await analyze(wtA);
+    const layout = layoutOf(wtA);
+    await cleanIn(wtA, {});
+    expect(existsSync(layout.checkoutSlot)).toBe(true);
+    expect(await commitDirs(layout)).toHaveLength(1);
+  }, 240_000);
+
+  it('clean --gc drops a deleted worktree and the graph only it referenced', async () => {
+    await analyze(wtA);
+    await fs.writeFile(path.join(wtB, 'b.ts'), 'export function beta() { return 2; }\n');
+    commitAll(wtB, 'b');
+    await analyze(wtB);
+    const layout = layoutOf(wtB);
+    const slotB = layout.checkoutSlot;
+    expect(await commitDirs(layout)).toHaveLength(2);
+
+    git(main, 'worktree', 'remove', '--force', wtB);
+    const logs = await cleanIn(main, { gc: true });
+
+    expect(existsSync(slotB)).toBe(false);
+    expect(await commitDirs(layout)).toHaveLength(1);
+    expect(existsSync(layoutOf(wtA).checkoutSlot)).toBe(true);
+    expect(logs.join('\n')).toMatch(/dropped 1 checkout\(s\), removed 1 commit graph/);
+  }, 240_000);
+});
+
+describe('reclaimSharedStore', () => {
+  let tmpHome: Awaited<ReturnType<typeof createTempDir>>;
+  let savedHome: string | undefined;
+
+  beforeEach(async () => {
+    tmpHome = await createTempDir('gitnexus-reclaim-home-');
+    savedHome = process.env.GITNEXUS_HOME;
+    process.env.GITNEXUS_HOME = tmpHome.dbPath;
+  });
+
+  afterEach(async () => {
+    if (savedHome === undefined) delete process.env.GITNEXUS_HOME;
+    else process.env.GITNEXUS_HOME = savedHome;
+    await tmpHome.cleanup();
+  });
+
+  const layout = (): SharedStoreLayout => sharedStoreLayout('repo-0123456789ab', '/tmp/wt');
+
+  const commitGraph = async (name: string): Promise<string> => {
+    const dir = path.join(layout().commitsDir, name);
+    await fs.mkdir(dir, { recursive: true });
+    await fs.writeFile(path.join(dir, 'lbug'), 'graph');
+    return dir;
+  };
+
+  const member = async (slotName: string, meta: Record<string, unknown>): Promise<string> => {
+    const slot = path.join(layout().checkoutsDir, slotName);
+    await fs.mkdir(slot, { recursive: true });
+    await saveMeta(slot, { lastCommit: '', indexedAt: '', repoPath: '/tmp/wt', ...meta });
+    return slot;
+  };
+
+  it('keeps referenced graphs and removes unreferenced graphs and stale staging', async () => {
+    const kept = await commitGraph('aaaaaaa-1111111111111111');
+    const orphan = await commitGraph('bbbbbbb-2222222222222222');
+    const staging = await commitGraph('.publish-dead');
+    await member('wt-000000000000', { graphPath: path.join(kept, 'lbug') });
+
+    const result = await reclaimSharedStore(layout().root);
+
+    expect(existsSync(kept)).toBe(true);
+    expect(existsSync(orphan)).toBe(false);
+    expect(existsSync(staging)).toBe(false);
+    expect(result.removed).toEqual([orphan]);
+    expect(result.storeRemoved).toBe(false);
+  });
+
+  it('never collects a slot whose metadata it cannot attribute', async () => {
+    const slot = path.join(layout().checkoutsDir, 'unknown-000000000000');
+    await fs.mkdir(slot, { recursive: true });
+    const result = await reclaimSharedStore(layout().root, { gc: true });
+    expect(existsSync(slot)).toBe(true);
+    expect(result.droppedMembers).toEqual([]);
+  });
+
+  it('is a no-op for storage outside the stores directory', async () => {
+    const outside = path.join(tmpHome.dbPath, 'elsewhere', '.gitnexus');
+    await fs.mkdir(outside, { recursive: true });
+    expect(await reclaimAfterSlotRemoval(outside)).toBeNull();
+    expect(existsSync(outside)).toBe(true);
+  });
+
+  it('reports a graph it cannot delete instead of failing', async () => {
+    const orphan = await commitGraph('ccccccc-3333333333333333');
+    await member('wt-000000000000', {});
+    const rm = vi.spyOn(fs, 'rm').mockImplementation(async (target) => {
+      if (String(target) === orphan) throw Object.assign(new Error('busy'), { code: 'EBUSY' });
+    });
+    try {
+      const result = await reclaimSharedStore(layout().root);
+      expect(result.kept).toEqual([orphan]);
+      expect(result.removed).toEqual([]);
+    } finally {
+      rm.mockRestore();
+    }
+  });
+});