diff --git a/scripts/clean.spec.ts b/scripts/clean.spec.ts
index 11a8c880b0..8e58c0ca44 100644
--- a/scripts/clean.spec.ts
+++ b/scripts/clean.spec.ts
@@ -82,6 +82,28 @@ describe('RepositoryCleaner', () => {
     expect(existsSync(join(root, 'native/system/tsconfig.tsbuildinfo'))).toBe(false)
   })
 
+  it('removes pnpm links to deleted packages and keeps live links', async () => {
+    const root = fixture()
+    const type = process.platform === 'win32' ? 'junction' : 'dir'
+    addProject(root, 'packages/core/live')
+    write(join(root, 'packages/core/live/package.json'), '{}')
+    const hoisted = join(root, 'node_modules/.pnpm/node_modules')
+    mkdirSync(join(hoisted, '@deepseek-ai'), { recursive: true })
+    symlinkSync(join(root, 'packages/core/live'), join(hoisted, '@deepseek-ai/dsh-live'), type)
+    symlinkSync(join(root, 'packages/hooks/gone'), join(hoisted, '@deepseek-ai/dsh-gone'), type)
+    symlinkSync(join(root, 'packages/hooks/plain'), join(hoisted, 'plain'), type)
+    symlinkSync(join(root, 'packages/hooks/top'), join(root, 'node_modules/top'), type)
+
+    const removed = await new RepositoryCleaner(root).clean()
+
+    expect(removed).toEqual([
+      'node_modules/.pnpm/node_modules/@deepseek-ai/dsh-gone',
+      'node_modules/.pnpm/node_modules/plain',
+      'node_modules/top',
+    ])
+    expect(existsSync(join(hoisted, '@deepseek-ai/dsh-live/package.json'))).toBe(true)
+  })
+
   it('refuses project outputs reached through a symlink outside the repository', async () => {
     const root = fixture()
     const externalProject = fixture()
diff --git a/scripts/clean.ts b/scripts/clean.ts
index bb789f298c..88e589e011 100644
--- a/scripts/clean.ts
+++ b/scripts/clean.ts
@@ -1,4 +1,4 @@
-import { lstat, readdir, realpath, rm } from 'node:fs/promises'
+import { lstat, readdir, realpath, rm, stat } from 'node:fs/promises'
 import { basename, dirname, isAbsolute, join, relative, resolve, sep } from 'node:path'
 import { fileURLToPath } from 'node:url'
 import ts from 'typescript'
@@ -10,9 +10,9 @@ function isMissing(error: unknown): boolean {
   return error instanceof Error && 'code' in error && error.code === 'ENOENT'
 }
 
-async function exists(path: string): Promise<boolean> {
+async function exists(path: string, probe: typeof lstat = lstat): Promise<boolean> {
   try {
-    await lstat(path)
+    await probe(path)
     return true
   } catch (error) {
     if (isMissing(error)) return false
@@ -30,6 +30,27 @@ async function childDirectories(path: string): Promise<string[]> {
   }
 }
 
+/** Lists symbolic links whose targets are missing in a node_modules directory and its `@scope` directories. */
+async function danglingLinks(modulesDirectory: string): Promise<string[]> {
+  const links: string[] = []
+  const scan = async (directory: string, scopes: boolean): Promise<void> => {
+    let entries
+    try {
+      entries = await readdir(directory, { withFileTypes: true })
+    } catch (error) {
+      if (isMissing(error)) return
+      throw error
+    }
+    for (const entry of entries) {
+      const path = join(directory, entry.name)
+      if (scopes && entry.isDirectory() && entry.name.startsWith('@')) await scan(path, false)
+      else if (entry.isSymbolicLink() && !await exists(path, stat)) links.push(path)
+    }
+  }
+  await scan(modulesDirectory, true)
+  return links
+}
+
 function repositoryPath(root: string, path: string): string {
   return relative(root, path).split(sep).join('/')
 }
@@ -88,6 +109,13 @@ export class RepositoryCleaner {
       await this.addIfPresent(targets, outputDirectory, canonicalRoot)
     }
 
+    // pnpm install keeps links whose targets are gone, such as hoisted links to deleted workspace packages.
+    for (const modulesDirectory of ['node_modules', 'node_modules/.pnpm/node_modules']) {
+      for (const link of await danglingLinks(join(this.root, modulesDirectory))) {
+        await this.addIfPresent(targets, link, canonicalRoot)
+      }
+    }
+
     for (const groupDirectory of await childDirectories(join(this.root, 'packages'))) {
       for (const packageDirectory of await childDirectories(groupDirectory)) {
         // A package.json marks a live package; its output was discovered from the