fix: prune should remove all cached metadata

.changeset/blue-monkeys-hear.md

@@ -0,0 +1,8 @@
+---
+"@pnpm/package-store": patch
+"@pnpm/plugin-commands-store": patch
+"@pnpm/store-connection-manager": patch
+"pnpm": patch
+---
+
+`pnpm store prune` should remove all cached metadata.

packages/package-store/src/storeController/index.ts

@@ -24,6 +24,7 @@ export default async function (
     importPackage?: ImportIndexedPackage
     pnpmVersion?: string
     ignoreFile?: (filename: string) => boolean
+    cacheDir: string
     storeDir: string
     networkConcurrency?: number
     packageImportMethod?: 'auto' | 'hardlink' | 'copy' | 'clone' | 'clone-or-copy'
@@ -50,7 +51,7 @@ export default async function (
     close: async () => {}, // eslint-disable-line:no-empty
     fetchPackage: packageRequester.fetchPackageToStore,
     importPackage: cafs.importPackage,
-    prune: prune.bind(null, storeDir),
+    prune: prune.bind(null, { storeDir, cacheDir: initOpts.cacheDir }),
     requestPackage: packageRequester.requestPackage,
     upload,
   }

packages/package-store/src/storeController/prune.ts

@@ -8,10 +8,18 @@ import ssri from 'ssri'
 
 const BIG_ONE = BigInt(1) as unknown
 
-export default async function prune (storeDir: string) {
+export interface PruneOptions {
+  cacheDir: string
+  storeDir: string
+}
+
+export default async function prune ({ cacheDir, storeDir }: PruneOptions) {
   const cafsDir = path.join(storeDir, 'files')
-  await rimraf(path.join(storeDir, 'metadata'))
-  await rimraf(path.join(storeDir, 'metadata-full'))
+  await Promise.all([
+    rimraf(path.join(cacheDir, 'metadata')),
+    rimraf(path.join(cacheDir, 'metadata-full')),
+    rimraf(path.join(cacheDir, 'metadata-full-filtered')),
+  ])
   await rimraf(path.join(storeDir, 'tmp'))
   globalInfo('Removed all cached metadata files')
   const pkgIndexFiles = [] as string[]

packages/package-store/test/index.ts

@@ -8,6 +8,7 @@ describe('store.importPackage()', () => {
   it('selects import method automatically', async () => {
     const tmp = tempy.directory()
     const storeDir = path.join(tmp, 'store')
+    const cacheDir = path.join(tmp, 'cache')
     const registry = 'https://registry.npmjs.org/'
     const authConfig = { registry }
     const { resolve, fetchers } = createClient({
@@ -16,6 +17,7 @@ describe('store.importPackage()', () => {
     })
     const storeController = await createStore(resolve, fetchers, {
       storeDir,
+      cacheDir,
       verifyStoreIntegrity: true,
     })
     const pkgId = 'registry.npmjs.org/is-positive/1.0.0'
@@ -43,6 +45,7 @@ describe('store.importPackage()', () => {
   it('uses copying', async () => {
     const tmp = tempy.directory()
     const storeDir = path.join(tmp, 'store')
+    const cacheDir = path.join(tmp, 'cache')
     const registry = 'https://registry.npmjs.org/'
     const authConfig = { registry }
     const { resolve, fetchers } = createClient({
@@ -52,6 +55,7 @@ describe('store.importPackage()', () => {
     const storeController = await createStore(resolve, fetchers, {
       packageImportMethod: 'copy',
       storeDir,
+      cacheDir,
       verifyStoreIntegrity: true,
     })
     const pkgId = 'registry.npmjs.org/is-positive/1.0.0'

packages/plugin-commands-store/test/storePrune.ts

@@ -19,8 +19,21 @@ test('remove unreferenced packages', async () => {
   const cacheDir = path.resolve('cache')
   const storeDir = path.resolve('store')
 
-  await execa('node', [pnpmBin, 'add', 'is-negative@2.1.0', '--store-dir', storeDir, '--registry', REGISTRY])
-  await execa('node', [pnpmBin, 'remove', 'is-negative', '--store-dir', storeDir, '--config.modules-cache-max-age=0'], { env: { npm_config_registry: REGISTRY } })
+  await execa('node', [
+    pnpmBin,
+    'add',
+    'is-negative@^2.1.0',
+    `--store-dir=${storeDir}`,
+    `--cache-dir=${cacheDir}`,
+    `--registry=${REGISTRY}`])
+  await execa('node', [
+    pnpmBin,
+    'remove',
+    'is-negative',
+    `--store-dir=${storeDir}`,
+    `--cache-dir=${cacheDir}`,
+    '--config.modules-cache-max-age=0',
+  ], { env: { npm_config_registry: REGISTRY } })
 
   await project.storeHas('is-negative', '2.1.0')
 
@@ -67,6 +80,7 @@ test('remove unreferenced packages', async () => {
       message: 'Removed 1 package',
     })
   )
+  expect(fs.readdirSync(cacheDir).length).toEqual(0)
 })
 
 test.skip('remove packages that are used by project that no longer exist', async () => {

packages/server/test/index.ts

@@ -19,12 +19,14 @@ async function createStoreController (storeDir?: string) {
     storeDir = path.join(tmp, 'store')
   }
   const authConfig = { registry }
+  const cacheDir = path.join(tmp, 'cache')
   const { resolve, fetchers } = createClient({
     authConfig,
-    cacheDir: path.join(tmp, 'cache'),
+    cacheDir,
   })
   return createStore(resolve, fetchers, {
     networkConcurrency: 1,
+    cacheDir,
     storeDir,
     verifyStoreIntegrity: true,
   })

packages/store-connection-manager/src/createNewStoreController.ts

@@ -86,6 +86,7 @@ export default async (
       importPackage: opts.hooks?.importPackage,
       networkConcurrency: opts.networkConcurrency,
       packageImportMethod: opts.packageImportMethod,
+      cacheDir: opts.cacheDir,
       storeDir: opts.storeDir,
       verifyStoreIntegrity: typeof opts.verifyStoreIntegrity === 'boolean'
         ? opts.verifyStoreIntegrity