feat: add cleanupUnusedCatalogs config (#9793)

.changeset/large-ducks-wear.md

@@ -0,0 +1,7 @@
+---
+"@pnpm/plugin-commands-installation": minor
+"@pnpm/workspace.manifest-writer": minor
+"pnpm": minor
+---
+
+Added the `cleanupUnusedCatalogs` configuration. When set to `true`, pnpm will remove unused catalog entries during installation [#9793](https://github.com/pnpm/pnpm/pull/9793).

config/config/src/Config.ts

@@ -152,6 +152,7 @@ export interface Config extends OptionsFromRootManifest {
   workspacePackagePatterns?: string[]
   catalogs?: Catalogs
   catalogMode?: 'strict' | 'prefer' | 'manual'
+  cleanupUnusedCatalogs?: boolean
   reporter?: string
   aggregateOutput: boolean
   linkWorkspacePackages: boolean | 'deep'

pkg-manager/core/src/install/extendInstallOptions.ts

@@ -29,6 +29,7 @@ export interface StrictInstallOptions {
   autoInstallPeersFromHighestMatch: boolean
   catalogs: Catalogs
   catalogMode: 'strict' | 'prefer' | 'manual'
+  cleanupUnusedCatalogs: boolean
   frozenLockfile: boolean
   frozenLockfileIfExists: boolean
   enableGlobalVirtualStore: boolean
@@ -244,6 +245,7 @@ const defaults = (opts: InstallOptions): StrictInstallOptions => {
       !process.setgid ||
       process.getuid?.() !== 0,
     catalogMode: 'manual',
+    cleanupUnusedCatalogs: false,
     useLockfile: true,
     saveLockfile: true,
     useGitBranchLockfile: false,

pkg-manager/plugin-commands-installation/src/installDeps.ts

@@ -54,6 +54,7 @@ export type InstallDepsOptions = Pick<Config,
 | 'bin'
 | 'catalogs'
 | 'catalogMode'
+| 'cleanupUnusedCatalogs'
 | 'cliOptions'
 | 'dedupePeerDependents'
 | 'depth'
@@ -321,6 +322,8 @@ when running add/update with the --workspace option')
         writeProjectManifest(updatedProject.manifest),
         updateWorkspaceManifest(opts.workspaceDir ?? opts.dir, {
           updatedCatalogs,
+          cleanupUnusedCatalogs: opts.cleanupUnusedCatalogs,
+          allProjects: opts.allProjects,
         }),
       ])
     }
@@ -346,6 +349,8 @@ when running add/update with the --workspace option')
       writeProjectManifest(updatedManifest),
       updateWorkspaceManifest(opts.workspaceDir ?? opts.dir, {
         updatedCatalogs,
+        cleanupUnusedCatalogs: opts.cleanupUnusedCatalogs,
+        allProjects,
       }),
     ])
   }

pkg-manager/plugin-commands-installation/src/recursive.ts

@@ -82,6 +82,7 @@ export type RecursiveOptions = CreateStoreControllerOptions & Pick<Config,
 | 'lockfileIncludeTarballUrl'
 | 'sharedWorkspaceLockfile'
 | 'tag'
+| 'cleanupUnusedCatalogs'
 > & {
   include?: IncludedDependencies
   includeDirect?: IncludedDependencies
@@ -293,6 +294,8 @@ export async function recursive (
       })
       promises.push(updateWorkspaceManifest(opts.workspaceDir, {
         updatedCatalogs,
+        cleanupUnusedCatalogs: opts.cleanupUnusedCatalogs,
+        allProjects,
       }))
       await Promise.all(promises)
     }
@@ -441,6 +444,8 @@ export async function recursive (
 
   await updateWorkspaceManifest(opts.workspaceDir, {
     updatedCatalogs,
+    cleanupUnusedCatalogs: opts.cleanupUnusedCatalogs,
+    allProjects,
   })
 
   if (

pnpm-lock.yaml

@@ -812,7 +812,7 @@ importers:
         version: link:../packages/logger
       '@pnpm/meta-updater':
         specifier: 'catalog:'
-        version: 2.0.6(@types/node@22.15.29)(typanion@3.14.0)
+        version: 2.0.6(@types/node@18.19.34)(typanion@3.14.0)
       '@pnpm/object.key-sorting':
         specifier: workspace:*
         version: link:../object/key-sorting
@@ -8496,6 +8496,9 @@ importers:
       '@pnpm/object.key-sorting':
         specifier: workspace:*
         version: link:../../object/key-sorting
+      '@pnpm/types':
+        specifier: workspace:*
+        version: link:../../packages/types
       '@pnpm/workspace.read-manifest':
         specifier: workspace:*
         version: link:../read-manifest
@@ -8506,6 +8509,12 @@ importers:
         specifier: 'catalog:'
         version: 5.0.0
     devDependencies:
+      '@pnpm/fs.find-packages':
+        specifier: workspace:*
+        version: link:../../fs/find-packages
+      '@pnpm/prepare':
+        specifier: workspace:*
+        version: link:../../__utils__/prepare
       '@pnpm/prepare-temp-dir':
         specifier: workspace:*
         version: link:../../__utils__/prepare-temp-dir
@@ -8840,10 +8849,6 @@ packages:
     peerDependencies:
       '@babel/core': ^7.0.0-0
 
-  '@babel/runtime@7.27.4':
-    resolution: {integrity: sha512-t3yaEOuGu9NlIZ+hIeGbBjFtZT7j2cb2tg0fuaJKeGotchRjjLfrBA9Kwf8quhpP1EUuxModQg04q/mBwyg8uA==}
-    engines: {node: '>=6.9.0'}
-
   '@babel/runtime@7.28.2':
     resolution: {integrity: sha512-KHp2IflsnGywDjBWDkR9iEqiWSpc8GIi0lgTT3mOElT0PP1tG26P4tmFI2YvAdzgq9RGyoHZQEIEdZy6Ec5xCA==}
     engines: {node: '>=6.9.0'}
@@ -15885,8 +15890,6 @@ snapshots:
     transitivePeerDependencies:
       - supports-color
 
-  '@babel/runtime@7.27.4': {}
-
   '@babel/runtime@7.28.2': {}
 
   '@babel/template@7.27.2':
@@ -16585,14 +16588,14 @@ snapshots:
       '@jest/test-result': 29.7.0
       '@jest/transform': 29.7.0(@babel/types@7.26.10)
       '@jest/types': 29.6.3
-      '@types/node': 18.19.34
+      '@types/node': 22.15.29
       ansi-escapes: 4.3.2
       chalk: 4.1.2
       ci-info: 3.9.0
       exit: 0.1.2
       graceful-fs: 4.2.11(patch_hash=68ebc232025360cb3dcd3081f4067f4e9fc022ab6b6f71a3230e86c7a5b337d1)
       jest-changed-files: 29.7.0
-      jest-config: 29.7.0(@babel/types@7.26.10)(@types/node@18.19.34)(ts-node@10.9.2(@types/node@18.19.34)(typescript@5.5.4))
+      jest-config: 29.7.0(@babel/types@7.26.10)(@types/node@22.15.29)(ts-node@10.9.2(@types/node@18.19.34)(typescript@5.5.4))
       jest-haste-map: 29.7.0
       jest-message-util: 29.7.0
       jest-regex-util: 29.6.3
@@ -16730,7 +16733,7 @@ snapshots:
       '@jest/schemas': 29.6.3
       '@types/istanbul-lib-coverage': 2.0.6
       '@types/istanbul-reports': 3.0.4
-      '@types/node': 18.19.34
+      '@types/node': 22.15.29
       '@types/yargs': 17.0.33
       chalk: 4.1.2
 
@@ -16796,7 +16799,7 @@ snapshots:
 
   '@npmcli/fs@4.0.0':
     dependencies:
-      semver: 7.7.1
+      semver: 7.7.2
 
   '@pkgjs/parseargs@0.11.0':
     optional: true
@@ -16866,28 +16869,6 @@ snapshots:
       - supports-color
       - typanion
 
-  '@pnpm/cli-utils@1000.1.5(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))(typanion@3.14.0)':
-    dependencies:
-      '@pnpm/cli-meta': 1000.0.8
-      '@pnpm/config': 1003.1.1(@pnpm/logger@1001.0.0)
-      '@pnpm/config.deps-installer': 1000.0.5(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))
-      '@pnpm/default-reporter': 1002.0.1(@pnpm/logger@1001.0.0)
-      '@pnpm/error': 1000.0.2
-      '@pnpm/logger': 1001.0.0
-      '@pnpm/manifest-utils': 1001.0.1(@pnpm/logger@1001.0.0)
-      '@pnpm/package-is-installable': 1000.0.10(@pnpm/logger@1001.0.0)
-      '@pnpm/pnpmfile': 1001.2.2(@pnpm/logger@1001.0.0)
-      '@pnpm/read-project-manifest': 1000.0.11
-      '@pnpm/store-connection-manager': 1002.0.3(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))(typanion@3.14.0)
-      '@pnpm/types': 1000.6.0
-      chalk: 4.1.2
-      load-json-file: 6.2.0
-    transitivePeerDependencies:
-      - '@pnpm/worker'
-      - domexception
-      - supports-color
-      - typanion
-
   '@pnpm/client@1000.0.19(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@18.19.34))(typanion@3.14.0)':
     dependencies:
       '@pnpm/default-resolver': 1002.0.2(@pnpm/logger@1001.0.0)
@@ -16907,25 +16888,6 @@ snapshots:
       - supports-color
       - typanion
 
-  '@pnpm/client@1000.0.19(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))(typanion@3.14.0)':
-    dependencies:
-      '@pnpm/default-resolver': 1002.0.2(@pnpm/logger@1001.0.0)
-      '@pnpm/directory-fetcher': 1000.1.7(@pnpm/logger@1001.0.0)
-      '@pnpm/fetch': 1000.2.2(@pnpm/logger@1001.0.0)
-      '@pnpm/fetching-types': 1000.1.0
-      '@pnpm/git-fetcher': 1001.0.8(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))(typanion@3.14.0)
-      '@pnpm/network.auth-header': 1000.0.3
-      '@pnpm/resolver-base': 1003.0.1
-      '@pnpm/tarball-fetcher': 1001.0.8(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))(typanion@3.14.0)
-      '@pnpm/types': 1000.6.0
-      ramda: '@pnpm/ramda@0.28.1'
-    transitivePeerDependencies:
-      - '@pnpm/logger'
-      - '@pnpm/worker'
-      - domexception
-      - supports-color
-      - typanion
-
   '@pnpm/colorize-semver-diff@1.0.1':
     dependencies:
       chalk: 4.1.2
@@ -16959,28 +16921,6 @@ snapshots:
       - domexception
       - supports-color
 
-  '@pnpm/config.deps-installer@1000.0.5(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))':
-    dependencies:
-      '@pnpm/config.config-writer': 1000.0.5
-      '@pnpm/core-loggers': 1001.0.1(@pnpm/logger@1001.0.0)
-      '@pnpm/error': 1000.0.2
-      '@pnpm/fetch': 1000.2.2(@pnpm/logger@1001.0.0)
-      '@pnpm/logger': 1001.0.0
-      '@pnpm/network.auth-header': 1000.0.3
-      '@pnpm/npm-resolver': 1004.0.1(@pnpm/logger@1001.0.0)
-      '@pnpm/package-store': 1002.0.4(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))
-      '@pnpm/parse-wanted-dependency': 1001.0.0
-      '@pnpm/pick-registry-for-package': 1000.0.8
-      '@pnpm/read-modules-dir': 1000.0.0
-      '@pnpm/read-package-json': 1000.0.9
-      '@pnpm/types': 1000.6.0
-      '@zkochan/rimraf': 3.0.2
-      get-npm-tarball-url: 2.1.0
-    transitivePeerDependencies:
-      - '@pnpm/worker'
-      - domexception
-      - supports-color
-
   '@pnpm/config.env-replace@1.1.0': {}
 
   '@pnpm/config.env-replace@3.0.1': {}
@@ -17290,19 +17230,6 @@ snapshots:
       - supports-color
       - typanion
 
-  '@pnpm/git-fetcher@1001.0.8(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))(typanion@3.14.0)':
-    dependencies:
-      '@pnpm/fetcher-base': 1000.0.11
-      '@pnpm/fs.packlist': 2.0.0
-      '@pnpm/logger': 1001.0.0
-      '@pnpm/prepare-package': 1000.0.16(@pnpm/logger@1001.0.0)(typanion@3.14.0)
-      '@pnpm/worker': 1000.1.7(@pnpm/logger@packages+logger)(@types/node@22.15.29)
-      '@zkochan/rimraf': 3.0.2
-      execa: safe-execa@0.1.2
-    transitivePeerDependencies:
-      - supports-color
-      - typanion
-
   '@pnpm/git-resolver@1001.0.2(@pnpm/logger@1001.0.0)':
     dependencies:
       '@pnpm/fetch': 1000.2.2(@pnpm/logger@1001.0.0)
@@ -17449,24 +17376,6 @@ snapshots:
       - supports-color
       - typanion
 
-  '@pnpm/meta-updater@2.0.6(@types/node@22.15.29)(typanion@3.14.0)':
-    dependencies:
-      '@pnpm/find-workspace-dir': 1000.1.0
-      '@pnpm/logger': 1001.0.0
-      '@pnpm/types': 1000.6.0
-      '@pnpm/worker': 1000.1.7(@pnpm/logger@packages+logger)(@types/node@22.15.29)
-      '@pnpm/workspace.find-packages': 1000.0.25(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))(typanion@3.14.0)
-      '@pnpm/workspace.read-manifest': 1000.1.5
-      load-json-file: 7.0.1
-      meow: 11.0.0
-      print-diff: 2.0.0
-      write-json-file: 5.0.0
-    transitivePeerDependencies:
-      - '@types/node'
-      - domexception
-      - supports-color
-      - typanion
-
   '@pnpm/network.agent@2.0.3':
     dependencies:
       '@pnpm/network.config': 2.1.0
@@ -17647,30 +17556,6 @@ snapshots:
       semver: 7.7.2
       ssri: 10.0.5
 
-  '@pnpm/package-requester@1004.0.2(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))':
-    dependencies:
-      '@pnpm/core-loggers': 1001.0.1(@pnpm/logger@1001.0.0)
-      '@pnpm/dependency-path': 1000.0.9
-      '@pnpm/error': 1000.0.2
-      '@pnpm/fetcher-base': 1000.0.11
-      '@pnpm/graceful-fs': 1000.0.0
-      '@pnpm/logger': 1001.0.0
-      '@pnpm/package-is-installable': 1000.0.10(@pnpm/logger@1001.0.0)
-      '@pnpm/pick-fetcher': 1000.0.0
-      '@pnpm/read-package-json': 1000.0.9
-      '@pnpm/resolver-base': 1003.0.1
-      '@pnpm/store-controller-types': 1003.0.2
-      '@pnpm/store.cafs': 1000.0.13
-      '@pnpm/types': 1000.6.0
-      '@pnpm/worker': 1000.1.7(@pnpm/logger@packages+logger)(@types/node@22.15.29)
-      p-defer: 3.0.0
-      p-limit: 3.1.0
-      p-queue: 6.6.2
-      promise-share: 1.0.0
-      ramda: '@pnpm/ramda@0.28.1'
-      semver: 7.7.2
-      ssri: 10.0.5
-
   '@pnpm/package-store@1002.0.4(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@18.19.34))':
     dependencies:
       '@pnpm/create-cafs-store': 1000.0.14(@pnpm/logger@1001.0.0)
@@ -17687,22 +17572,6 @@ snapshots:
       ramda: '@pnpm/ramda@0.28.1'
       ssri: 10.0.5
 
-  '@pnpm/package-store@1002.0.4(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))':
-    dependencies:
-      '@pnpm/create-cafs-store': 1000.0.14(@pnpm/logger@1001.0.0)
-      '@pnpm/fetcher-base': 1000.0.11
-      '@pnpm/logger': 1001.0.0
-      '@pnpm/package-requester': 1004.0.2(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))
-      '@pnpm/resolver-base': 1003.0.1
-      '@pnpm/store-controller-types': 1003.0.2
-      '@pnpm/store.cafs': 1000.0.13
-      '@pnpm/types': 1000.6.0
-      '@pnpm/worker': 1000.1.7(@pnpm/logger@packages+logger)(@types/node@22.15.29)
-      '@zkochan/rimraf': 3.0.2
-      load-json-file: 6.2.0
-      ramda: '@pnpm/ramda@0.28.1'
-      ssri: 10.0.5
-
   '@pnpm/parse-overrides@1000.0.2':
     dependencies:
       '@pnpm/catalogs.resolver': 1000.0.2
@@ -17919,25 +17788,6 @@ snapshots:
       - supports-color
       - typanion
 
-  '@pnpm/store-connection-manager@1002.0.3(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))(typanion@3.14.0)':
-    dependencies:
-      '@pnpm/cli-meta': 1000.0.8
-      '@pnpm/client': 1000.0.19(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))(typanion@3.14.0)
-      '@pnpm/config': 1003.1.1(@pnpm/logger@1001.0.0)
-      '@pnpm/error': 1000.0.2
-      '@pnpm/logger': 1001.0.0
-      '@pnpm/package-store': 1002.0.4(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))
-      '@pnpm/server': 1001.0.4(@pnpm/logger@1001.0.0)
-      '@pnpm/store-path': 1000.0.2
-      '@zkochan/diable': 1.0.2
-      delay: 5.0.0
-      dir-is-case-sensitive: 2.0.0
-    transitivePeerDependencies:
-      - '@pnpm/worker'
-      - domexception
-      - supports-color
-      - typanion
-
   '@pnpm/store-controller-types@1001.0.3':
     dependencies:
       '@pnpm/fetcher-base': 1000.0.5
@@ -18011,28 +17861,6 @@ snapshots:
       - supports-color
       - typanion
 
-  '@pnpm/tarball-fetcher@1001.0.8(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))(typanion@3.14.0)':
-    dependencies:
-      '@pnpm/core-loggers': 1001.0.1(@pnpm/logger@1001.0.0)
-      '@pnpm/error': 1000.0.2
-      '@pnpm/fetcher-base': 1000.0.11
-      '@pnpm/fetching-types': 1000.1.0
-      '@pnpm/fs.packlist': 2.0.0
-      '@pnpm/graceful-fs': 1000.0.0
-      '@pnpm/logger': 1001.0.0
-      '@pnpm/prepare-package': 1000.0.16(@pnpm/logger@1001.0.0)(typanion@3.14.0)
-      '@pnpm/worker': 1000.1.7(@pnpm/logger@packages+logger)(@types/node@22.15.29)
-      '@zkochan/retry': 0.2.0
-      lodash.throttle: 4.1.1
-      p-map-values: 1.0.0
-      path-temp: 2.1.0
-      ramda: '@pnpm/ramda@0.28.1'
-      rename-overwrite: 6.0.3
-    transitivePeerDependencies:
-      - domexception
-      - supports-color
-      - typanion
-
   '@pnpm/tarball-resolver@1002.0.2':
     dependencies:
       '@pnpm/fetching-types': 1000.1.0
@@ -18080,26 +17908,6 @@ snapshots:
     transitivePeerDependencies:
       - '@types/node'
 
-  '@pnpm/worker@1000.1.7(@pnpm/logger@packages+logger)(@types/node@22.15.29)':
-    dependencies:
-      '@pnpm/cafs-types': 1000.0.0
-      '@pnpm/create-cafs-store': 1000.0.14(@pnpm/logger@1001.0.0)
-      '@pnpm/crypto.polyfill': 1000.1.0
-      '@pnpm/error': 1000.0.2
-      '@pnpm/exec.pkg-requires-build': 1000.0.8
-      '@pnpm/fs.hard-link-dir': 1000.0.1(@pnpm/logger@1001.0.0)
-      '@pnpm/graceful-fs': 1000.0.0
-      '@pnpm/logger': link:packages/logger
-      '@pnpm/store.cafs': 1000.0.13
-      '@pnpm/symlink-dependency': 1000.0.9(@pnpm/logger@1001.0.0)
-      '@rushstack/worker-pool': 0.4.9(@types/node@22.15.29)
-      is-windows: 1.0.2
-      load-json-file: 6.2.0
-      p-limit: 3.1.0
-      shell-quote: 1.8.3
-    transitivePeerDependencies:
-      - '@types/node'
-
   '@pnpm/workspace.find-packages@1000.0.15(@pnpm/logger@1000.0.0)':
     dependencies:
       '@pnpm/cli-utils': 1000.0.15(@pnpm/logger@1000.0.0)
@@ -18123,20 +17931,6 @@ snapshots:
       - supports-color
       - typanion
 
-  '@pnpm/workspace.find-packages@1000.0.25(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))(typanion@3.14.0)':
-    dependencies:
-      '@pnpm/cli-utils': 1000.1.5(@pnpm/logger@1001.0.0)(@pnpm/worker@1000.1.7(@pnpm/logger@1001.0.0)(@types/node@22.15.29))(typanion@3.14.0)
-      '@pnpm/constants': 1001.1.0
-      '@pnpm/fs.find-packages': 1000.0.11
-      '@pnpm/logger': 1001.0.0
-      '@pnpm/types': 1000.6.0
-      '@pnpm/util.lex-comparator': 3.0.2
-    transitivePeerDependencies:
-      - '@pnpm/worker'
-      - domexception
-      - supports-color
-      - typanion
-
   '@pnpm/workspace.manifest-writer@1000.1.4':
     dependencies:
       '@pnpm/constants': 1001.1.0
@@ -18338,7 +18132,7 @@ snapshots:
 
   '@types/isexe@2.0.2':
     dependencies:
-      '@types/node': 18.19.34
+      '@types/node': 22.15.29
 
   '@types/istanbul-lib-coverage@2.0.6': {}
 
@@ -18461,7 +18255,7 @@ snapshots:
 
   '@types/touch@3.1.5':
     dependencies:
-      '@types/node': 18.19.34
+      '@types/node': 22.15.29
 
   '@types/treeify@1.0.3': {}
 
@@ -19817,7 +19611,7 @@ snapshots:
 
   date-fns@2.30.0:
     dependencies:
-      '@babel/runtime': 7.27.4
+      '@babel/runtime': 7.28.2
 
   dayjs@1.11.7: {}
 
@@ -19922,7 +19716,7 @@ snapshots:
 
   didyoumean2@6.0.1:
     dependencies:
-      '@babel/runtime': 7.27.4
+      '@babel/runtime': 7.28.2
       fastest-levenshtein: 1.0.16
       lodash.deburr: 4.1.0
 
@@ -21529,6 +21323,38 @@ snapshots:
       - babel-plugin-macros
       - supports-color
 
+  jest-config@29.7.0(@babel/types@7.26.10)(@types/node@22.15.29)(ts-node@10.9.2(@types/node@18.19.34)(typescript@5.5.4)):
+    dependencies:
+      '@babel/core': 7.26.10
+      '@jest/test-sequencer': 29.7.0
+      '@jest/types': 29.6.3
+      babel-jest: 29.7.0(@babel/core@7.26.10)(@babel/types@7.26.10)
+      chalk: 4.1.2
+      ci-info: 3.9.0
+      deepmerge: 4.3.1
+      glob: 7.2.3
+      graceful-fs: 4.2.11(patch_hash=68ebc232025360cb3dcd3081f4067f4e9fc022ab6b6f71a3230e86c7a5b337d1)
+      jest-circus: 29.7.0(@babel/types@7.26.10)
+      jest-environment-node: 29.7.0
+      jest-get-type: 29.6.3
+      jest-regex-util: 29.6.3
+      jest-resolve: 29.7.0
+      jest-runner: 29.7.0(@babel/types@7.26.10)
+      jest-util: 29.7.0
+      jest-validate: 29.7.0
+      micromatch: 4.0.8
+      parse-json: 5.2.0
+      pretty-format: 29.7.0
+      slash: 3.0.0
+      strip-json-comments: 3.1.1
+    optionalDependencies:
+      '@types/node': 22.15.29
+      ts-node: 10.9.2(@types/node@18.19.34)(typescript@5.5.4)
+    transitivePeerDependencies:
+      - '@babel/types'
+      - babel-plugin-macros
+      - supports-color
+
   jest-diff@29.7.0:
     dependencies:
       chalk: 4.1.2
@@ -21713,7 +21539,7 @@ snapshots:
   jest-util@29.7.0:
     dependencies:
       '@jest/types': 29.6.3
-      '@types/node': 18.19.34
+      '@types/node': 22.15.29
       chalk: 4.1.2
       ci-info: 3.9.0
       graceful-fs: 4.2.11(patch_hash=68ebc232025360cb3dcd3081f4067f4e9fc022ab6b6f71a3230e86c7a5b337d1)
@@ -22350,7 +22176,7 @@ snapshots:
       make-fetch-happen: 14.0.3
       nopt: 8.1.0
       proc-log: 5.0.0
-      semver: 7.7.1
+      semver: 7.7.2
       tar: 7.4.3
       which: 5.0.0
     transitivePeerDependencies:
@@ -23266,7 +23092,7 @@ snapshots:
   semver-range-intersect@0.3.1:
     dependencies:
       '@types/semver': 6.2.7
-      semver: 7.7.1
+      semver: 7.7.2
 
   semver-utils@1.1.4: {}
 
@@ -24203,7 +24029,7 @@ snapshots:
 
   version-selector-type@3.0.0:
     dependencies:
-      semver: 7.7.1
+      semver: 7.7.2
 
   vfile-message@2.0.4:
     dependencies:

workspace/manifest-writer/package.json

@@ -35,11 +35,14 @@
     "@pnpm/constants": "workspace:*",
     "@pnpm/lockfile.types": "workspace:*",
     "@pnpm/object.key-sorting": "workspace:*",
+    "@pnpm/types": "workspace:*",
     "@pnpm/workspace.read-manifest": "workspace:*",
     "ramda": "catalog:",
     "write-yaml-file": "catalog:"
   },
   "devDependencies": {
+    "@pnpm/fs.find-packages": "workspace:*",
+    "@pnpm/prepare": "workspace:*",
     "@pnpm/prepare-temp-dir": "workspace:*",
     "@pnpm/workspace.manifest-writer": "workspace:*",
     "@types/ramda": "catalog:",

workspace/manifest-writer/src/index.ts

@@ -7,6 +7,9 @@ import { WORKSPACE_MANIFEST_FILENAME } from '@pnpm/constants'
 import writeYamlFile from 'write-yaml-file'
 import equals from 'ramda/src/equals'
 import { sortKeysByPriority } from '@pnpm/object.key-sorting'
+import {
+  type Project,
+} from '@pnpm/types'
 
 async function writeManifestFile (dir: string, manifest: Partial<WorkspaceManifest>): Promise<void> {
   manifest = sortKeysByPriority({
@@ -25,9 +28,14 @@ async function writeManifestFile (dir: string, manifest: Partial<WorkspaceManife
 export async function updateWorkspaceManifest (dir: string, opts: {
   updatedFields?: Partial<WorkspaceManifest>
   updatedCatalogs?: Catalogs
+  cleanupUnusedCatalogs?: boolean
+  allProjects?: Project[]
 }): Promise<void> {
   const manifest = await readWorkspaceManifest(dir) ?? {} as WorkspaceManifest
   let shouldBeUpdated = opts.updatedCatalogs != null && addCatalogs(manifest, opts.updatedCatalogs)
+  if (opts.cleanupUnusedCatalogs) {
+    shouldBeUpdated = removePackagesFromWorkspaceCatalog(manifest, opts.allProjects ?? []) || shouldBeUpdated
+  }
 
   for (const [key, value] of Object.entries(opts.updatedFields ?? {})) {
     if (!equals(manifest[key as keyof WorkspaceManifest], value)) {
@@ -90,3 +98,83 @@ function addCatalogs (manifest: Partial<WorkspaceManifest>, newCatalogs: Catalog
 
   return shouldBeUpdated
 }
+
+function removePackagesFromWorkspaceCatalog (manifest: Partial<WorkspaceManifest>, packagesJson: Project[]): boolean {
+  let shouldBeUpdated = false
+
+  if (manifest.catalog == null && manifest.catalogs == null) {
+    return shouldBeUpdated
+  }
+  const packageReferences: Record<string, Set<string>> = {}
+
+  for (const pkg of packagesJson) {
+    const pkgManifest = pkg.manifest
+    const dependencyTypes = [
+      pkgManifest.dependencies,
+      pkgManifest.devDependencies,
+      pkgManifest.optionalDependencies,
+      pkgManifest.peerDependencies,
+    ]
+
+    for (const deps of dependencyTypes) {
+      if (!deps) continue
+
+      for (const [pkgName, version] of Object.entries(deps)) {
+        if (!packageReferences[pkgName]) {
+          packageReferences[pkgName] = new Set()
+        }
+        packageReferences[pkgName].add(version)
+      }
+    }
+  }
+
+  if (manifest.catalog) {
+    const packagesToRemove = Object.keys(manifest.catalog).filter(pkg =>
+      !packageReferences[pkg]?.has('catalog:')
+    )
+
+    for (const pkg of packagesToRemove) {
+      delete manifest.catalog![pkg]
+      shouldBeUpdated = true
+    }
+
+    if (Object.keys(manifest.catalog).length === 0) {
+      delete manifest.catalog
+      shouldBeUpdated = true
+    }
+  }
+
+  if (manifest.catalogs) {
+    const catalogsToRemove: string[] = []
+
+    for (const [catalogName, catalog] of Object.entries(manifest.catalogs)) {
+      if (!catalog) continue
+
+      const packagesToRemove = Object.keys(catalog).filter(pkg => {
+        const references = packageReferences[pkg]
+        return !references?.has(`catalog:${catalogName}`) && !references?.has('catalog:')
+      })
+
+      for (const pkg of packagesToRemove) {
+        delete catalog[pkg]
+        shouldBeUpdated = true
+      }
+
+      if (Object.keys(catalog).length === 0) {
+        catalogsToRemove.push(catalogName)
+        shouldBeUpdated = true
+      }
+    }
+
+    for (const catalogName of catalogsToRemove) {
+      delete manifest.catalogs[catalogName]
+    }
+
+    if (Object.keys(manifest.catalogs).length === 0) {
+      delete manifest.catalogs
+      shouldBeUpdated = true
+    }
+  }
+
+  return shouldBeUpdated
+}

workspace/manifest-writer/test/removeCatalogs.test.ts

@@ -0,0 +1,298 @@
+import path from 'path'
+import fs from 'fs'
+import { WORKSPACE_MANIFEST_FILENAME } from '@pnpm/constants'
+import { tempDir } from '@pnpm/prepare-temp-dir'
+import { prepare } from '@pnpm/prepare'
+import { updateWorkspaceManifest } from '@pnpm/workspace.manifest-writer'
+import { sync as readYamlFile } from 'read-yaml-file'
+import { sync as writeYamlFile } from 'write-yaml-file'
+import { findPackages } from '@pnpm/fs.find-packages'
+
+test('remove the default catalog if it is empty', async () => {
+  const dir = tempDir(false)
+  const filePath = path.join(dir, WORKSPACE_MANIFEST_FILENAME)
+  prepare({
+    dependencies: {
+      foo: '^0.1.2',
+    },
+  }, { tempDir: dir })
+  const allProjects = await findPackages(dir)
+  await updateWorkspaceManifest(dir, {
+    updatedCatalogs: {
+      default: {},
+    },
+    allProjects,
+  })
+  await updateWorkspaceManifest(dir, {
+    updatedCatalogs: {
+      default: {
+        foo: '^0.1.2',
+      },
+    },
+  })
+  expect(readYamlFile(filePath)).toStrictEqual({
+    catalog: {
+      foo: '^0.1.2',
+    },
+  })
+  await updateWorkspaceManifest(dir, {
+    cleanupUnusedCatalogs: true,
+    allProjects,
+  })
+  expect(fs.existsSync(filePath)).toBeFalsy()
+})
+
+test('remove the unused default catalog', async () => {
+  const dir = tempDir(false)
+  const filePath = path.join(dir, WORKSPACE_MANIFEST_FILENAME)
+  writeYamlFile(filePath, {
+    catalog: {
+      bar: '3.2.1',
+    },
+  })
+  await updateWorkspaceManifest(dir, {
+    updatedCatalogs: {
+      default: {
+        foo: '^0.1.2',
+      },
+    },
+  })
+  expect(readYamlFile(filePath)).toStrictEqual({
+    catalog: {
+      bar: '3.2.1',
+      foo: '^0.1.2',
+    },
+  })
+  prepare({
+    dependencies: {
+      foo: '^0.1.2',
+      bar: 'catalog:',
+    },
+  }, { tempDir: dir })
+  const allProjects = await findPackages(dir)
+  await updateWorkspaceManifest(dir, {
+    cleanupUnusedCatalogs: true,
+    allProjects,
+  })
+  expect(readYamlFile(filePath)).toStrictEqual({
+    catalog: {
+      bar: '3.2.1',
+    },
+  })
+})
+
+test('remove the unused default catalog with catalogs', async () => {
+  const dir = tempDir(false)
+  const filePath = path.join(dir, WORKSPACE_MANIFEST_FILENAME)
+  writeYamlFile(filePath, {
+    catalogs: {
+      default: {
+        bar: '3.2.1',
+      },
+    },
+  })
+  await updateWorkspaceManifest(dir, {
+    updatedCatalogs: {
+      default: {
+        foo: '^0.1.2',
+      },
+    },
+  })
+  expect(readYamlFile(filePath)).toStrictEqual({
+    catalogs: {
+      default: {
+        bar: '3.2.1',
+        foo: '^0.1.2',
+      },
+    },
+  })
+  prepare({
+    dependencies: {
+      foo: '^0.1.2',
+      bar: 'catalog:',
+    },
+  }, { tempDir: dir })
+  const allProjects = await findPackages(dir)
+  await updateWorkspaceManifest(dir, {
+    cleanupUnusedCatalogs: true,
+    allProjects,
+  })
+  expect(readYamlFile(filePath)).toStrictEqual({
+    catalogs: {
+      default: {
+        bar: '3.2.1',
+      },
+    },
+  })
+})
+
+test('remove the unused named catalog', async () => {
+  const dir = tempDir(false)
+  const filePath = path.join(dir, WORKSPACE_MANIFEST_FILENAME)
+  await updateWorkspaceManifest(dir, {
+    updatedCatalogs: {
+      foo: {
+        abc: '0.1.2',
+      },
+      bar: {
+        def: '3.2.1',
+      },
+    },
+  })
+  expect(readYamlFile(filePath)).toStrictEqual({
+    catalogs: {
+      foo: {
+        abc: '0.1.2',
+      },
+      bar: {
+        def: '3.2.1',
+      },
+    },
+  })
+  prepare({
+    dependencies: {
+      abc: '0.1.2',
+      def: 'catalog:bar',
+    },
+  }, { tempDir: dir })
+  const allProjects = await findPackages(dir)
+  await updateWorkspaceManifest(dir, {
+    cleanupUnusedCatalogs: true,
+    allProjects,
+  })
+  expect(readYamlFile(filePath)).toStrictEqual({
+    catalogs: {
+      bar: {
+        def: '3.2.1',
+      },
+    },
+  })
+})
+
+test('remove all unused named catalogs', async () => {
+  const dir = tempDir(false)
+  const filePath = path.join(dir, WORKSPACE_MANIFEST_FILENAME)
+  writeYamlFile(filePath, {
+    catalogs: {
+      foo: {
+        ghi: '7.8.9',
+      },
+    },
+  })
+  await updateWorkspaceManifest(dir, {
+    updatedCatalogs: {
+      foo: {
+        abc: '0.1.2',
+      },
+      bar: {
+        def: '3.2.1',
+      },
+    },
+  })
+  expect(readYamlFile(filePath)).toStrictEqual({
+    catalogs: {
+      foo: {
+        abc: '0.1.2',
+        ghi: '7.8.9',
+      },
+      bar: {
+        def: '3.2.1',
+      },
+    },
+  })
+  prepare({
+    dependencies: {
+      def: 'catalog:bar',
+      ghi: 'catalog:foo',
+    },
+  }, { tempDir: dir })
+  const allProjects = await findPackages(dir)
+
+  await updateWorkspaceManifest(dir, {
+    cleanupUnusedCatalogs: true,
+    allProjects,
+  })
+  expect(readYamlFile(filePath)).toStrictEqual({
+    catalogs: {
+      bar: {
+        def: '3.2.1',
+      },
+      foo: {
+        ghi: '7.8.9',
+      },
+    },
+  })
+  prepare({
+    dependencies: {
+      def: '3.2.1',
+    },
+  }, { tempDir: dir })
+  const _allProjects = await findPackages(dir)
+  await updateWorkspaceManifest(dir, {
+    cleanupUnusedCatalogs: true,
+    allProjects: _allProjects,
+  })
+  expect(fs.existsSync(filePath)).toBeFalsy()
+})
+
+test('same pkg with different version', async () => {
+  const dir = tempDir(false)
+  const filePath = path.join(dir, WORKSPACE_MANIFEST_FILENAME)
+  writeYamlFile(filePath, {
+    catalogs: {
+      foo: {
+        ghi: '7.8.9',
+      },
+    },
+  })
+  await updateWorkspaceManifest(dir, {
+    updatedCatalogs: {
+      foo: {
+        abc: '0.1.2',
+      },
+      bar: {
+        def: '3.2.1',
+        abc: '1.2.3',
+      },
+    },
+  })
+  expect(readYamlFile(filePath)).toStrictEqual({
+    catalogs: {
+      foo: {
+        abc: '0.1.2',
+        ghi: '7.8.9',
+      },
+      bar: {
+        def: '3.2.1',
+        abc: '1.2.3',
+      },
+    },
+  })
+  prepare({
+    dependencies: {
+      def: 'catalog:bar',
+      ghi: 'catalog:foo',
+      abc: 'catalog:foo',
+    },
+    optionalDependencies: {
+      abc: 'catalog:bar',
+    },
+  }, { tempDir: dir })
+  const allProjects = await findPackages(dir)
+  await updateWorkspaceManifest(dir, {
+    cleanupUnusedCatalogs: true,
+    allProjects,
+  })
+  expect(readYamlFile(filePath)).toStrictEqual({
+    catalogs: {
+      bar: {
+        abc: '1.2.3',
+        def: '3.2.1',
+      },
+      foo: {
+        abc: '0.1.2',
+        ghi: '7.8.9',
+      },
+    },
+  })
+})

workspace/manifest-writer/tsconfig.json

@@ -9,12 +9,18 @@
     "../../__typings__/**/*.d.ts"
   ],
   "references": [
+    {
+      "path": "../../__utils__/prepare"
+    },
     {
       "path": "../../__utils__/prepare-temp-dir"
     },
     {
       "path": "../../catalogs/types"
     },
+    {
+      "path": "../../fs/find-packages"
+    },
     {
       "path": "../../lockfile/types"
     },
@@ -24,6 +30,9 @@
     {
       "path": "../../packages/constants"
     },
+    {
+      "path": "../../packages/types"
+    },
     {
       "path": "../read-manifest"
     }