fix: stop install from recreating node_modules after pnpm fetch (#11490)

Closes #11488.

`pnpm fetch` writes forced-empty `hoistPattern: []` and `publicHoistPattern: []` into `.modules.yaml` (because its `virtualStoreOnly` install path skips hoisting). In v10 the follow-up `pnpm install` ignored these unless the user had explicitly set a hoist-pattern in their config. v11's [#11199](https://github.com/pnpm/pnpm/pull/11199) removed that explicit-config gate, so `validateModules` now always sees the empty patterns as a hoist-pattern change and purges `node_modules` — slow on every CI run, and per the bug report sometimes leaves the modules dir in an `ERR_MODULE_NOT_FOUND` state on subsequent runs.

The fix marks `.modules.yaml` with a new `virtualStoreOnly: true` field after a fetch. `validateModules` recognizes this flag as "incomplete install state" and skips the `PUBLIC_HOIST_PATTERN_DIFF` / `HOIST_PATTERN_DIFF` comparisons. The next install then completes the missing post-import linking in place rather than purging. The flag is dropped from `.modules.yaml` once a normal install runs.

A genuine hoist-pattern change (without a fetch in between) still triggers the purge as before — verified manually with `publicHoistPattern` in `pnpm-workspace.yaml`.

.changeset/fetch-install-no-recreate.md

@@ -0,0 +1,8 @@
+---
+"@pnpm/installing.modules-yaml": patch
+"@pnpm/installing.deps-restorer": patch
+"@pnpm/installing.deps-installer": patch
+"pnpm": patch
+---
+
+Fix `pnpm install` recreating `node_modules` after `pnpm fetch`. `pnpm fetch` records empty `hoistPattern` and `publicHoistPattern` in `.modules.yaml`; since v11 removed the explicit-config gate, the follow-up install treated those as a hoist-pattern change and purged the modules directory. The fetch step now flags the modules manifest with `virtualStoreOnly: true` so the next install skips the hoist-pattern comparison and completes the missing post-import linking in place [#11488](https://github.com/pnpm/pnpm/issues/11488).

installing/commands/src/install.ts

@@ -284,6 +284,8 @@ export type InstallCommandOptions = Pick<Config,
 | 'frozenLockfile'
 | 'global'
 | 'globalPnpmfile'
+| 'hoistPattern'
+| 'publicHoistPattern'
 | 'ignorePnpmfile'
 | 'ignoreScripts'
 | 'injectWorkspacePackages'

installing/commands/test/fetch.ts

@@ -230,6 +230,68 @@ test('fetch populates global virtual store links/', async () => {
   expect(entries.length).toBeGreaterThan(0)
 })
 
+// Regression test for https://github.com/pnpm/pnpm/issues/11488
+// A subsequent install must not purge node_modules just because fetch
+// recorded forced-empty hoist patterns in .modules.yaml. The follow-up
+// install must also complete the post-import linking that fetch skipped:
+// importer symlinks at the project root and hoisting under .pnpm/node_modules.
+test('install after fetch completes linking without recreating node_modules', async () => {
+  const project = prepare({
+    dependencies: { '@pnpm.e2e/pkg-with-1-dep': '100.0.0' },
+  })
+  const storeDir = path.resolve('store')
+
+  // Generate the lockfile only — no need for a full install
+  await install.handler({
+    ...DEFAULT_OPTIONS,
+    cacheDir: path.resolve('cache'),
+    dir: process.cwd(),
+    linkWorkspacePackages: true,
+    lockfileOnly: true,
+    storeDir,
+  })
+
+  await fetch.handler({
+    ...DEFAULT_OPTIONS,
+    cacheDir: path.resolve('cache'),
+    dir: process.cwd(),
+    storeDir,
+  })
+
+  const modulesYamlPath = path.resolve(project.dir(), 'node_modules/.modules.yaml')
+  const virtualStoreDir = path.resolve(project.dir(), 'node_modules/.pnpm')
+  const virtualStoreInodeBefore = fs.statSync(virtualStoreDir).ino
+  // fetch only populates the virtual store — no importer symlink and no
+  // hoisting yet.
+  expect(fs.existsSync(path.resolve(project.dir(), 'node_modules/@pnpm.e2e/pkg-with-1-dep'))).toBeFalsy()
+  expect(fs.existsSync(path.resolve(virtualStoreDir, 'node_modules/@pnpm.e2e/dep-of-pkg-with-1-dep'))).toBeFalsy()
+  // fetch records the marker that opts the next install out of hoist-pattern checks.
+  expect(JSON.parse(fs.readFileSync(modulesYamlPath, 'utf8')).virtualStoreOnly).toBe(true)
+
+  await install.handler({
+    ...DEFAULT_OPTIONS,
+    cacheDir: path.resolve('cache'),
+    dir: process.cwd(),
+    frozenLockfile: true,
+    hoistPattern: ['*'],
+    linkWorkspacePackages: true,
+    storeDir,
+    preferOffline: true,
+  })
+
+  // If the modules dir had been purged, the directory's inode would change
+  // (rimraf + remake creates a new directory).
+  expect(fs.statSync(virtualStoreDir).ino).toBe(virtualStoreInodeBefore)
+  // The direct dep must be symlinked at the project root.
+  expect(fs.existsSync(path.resolve(project.dir(), 'node_modules/@pnpm.e2e/pkg-with-1-dep'))).toBeTruthy()
+  // The transitive dep must be hoisted under the virtual store
+  // (default hoistPattern is ['*']).
+  expect(fs.existsSync(path.resolve(virtualStoreDir, 'node_modules/@pnpm.e2e/dep-of-pkg-with-1-dep'))).toBeTruthy()
+  // The marker must be cleared once the install completes the linking,
+  // otherwise a later install would keep skipping hoist-pattern checks.
+  expect(JSON.parse(fs.readFileSync(modulesYamlPath, 'utf8')).virtualStoreOnly).toBeUndefined()
+})
+
 test('fetch applies patches to dependencies when patchedDependencies key is bare package name', async () => {
   const f = fixtures(import.meta.dirname)
   const project = prepare({

installing/deps-installer/src/install/index.ts

@@ -1601,6 +1601,7 @@ const _installInContext: InstallFunction = async (projects, ctx, opts) => {
           packageManager: `${opts.packageManager.name}@${opts.packageManager.version}`,
           pendingBuilds: ctx.pendingBuilds,
           publicHoistPattern: ctx.publicHoistPattern,
+          virtualStoreOnly: opts.virtualStoreOnly,
           prunedAt: opts.pruneVirtualStore || ctx.modulesFile == null
             ? new Date().toUTCString()
             : ctx.modulesFile.prunedAt,

installing/deps-installer/src/install/validateModules.ts

@@ -62,7 +62,10 @@ export async function validateModules (
       ' Run "pnpm install" to recreate the modules directory.'
     )
   }
+  // virtualStoreOnly installs (e.g. `pnpm fetch`) force empty hoist patterns
+  // into .modules.yaml; the follow-up install must complete linking, not purge.
   if (
+    !modules.virtualStoreOnly &&
     !equals(modules.publicHoistPattern ?? [], opts.publicHoistPattern ?? [])
   ) {
     if (opts.forceNewModules && (rootProject != null)) {
@@ -78,7 +81,7 @@ export async function validateModules (
 
   const importersToPurge: ImporterToPurge[] = []
 
-  if (rootProject != null) {
+  if (!modules.virtualStoreOnly && rootProject != null) {
     try {
       if (!equals(opts.currentHoistPattern ?? [], opts.hoistPattern ?? [])) {
         throw new PnpmError(

installing/deps-restorer/src/index.ts

@@ -676,6 +676,7 @@ export async function headlessInstall (opts: HeadlessOptions): Promise<Installat
       virtualStoreDir,
       virtualStoreDirMaxLength: opts.virtualStoreDirMaxLength,
       allowBuilds: opts.allowBuilds,
+      virtualStoreOnly: opts.virtualStoreOnly,
     })
     const currentLockfileDir = path.join(rootModulesDir, '.pnpm')
     if (opts.useLockfile) {

installing/modules-yaml/src/index.ts

@@ -41,6 +41,10 @@ interface ModulesRaw {
   injectedDeps?: Record<string, string[]>
   hoistedLocations?: Record<string, string[]>
   allowBuilds?: Record<string, boolean | string>
+  // True when the modules dir was populated by a virtualStoreOnly install
+  // (e.g. `pnpm fetch`) — the recorded hoist patterns are forced empty
+  // and must not be compared against user config on the next install.
+  virtualStoreOnly?: boolean
 }
 
 export type Modules = Omit<ModulesRaw, 'ignoredBuilds'> & {
@@ -123,6 +127,9 @@ export async function writeModulesManifest (
   if (saveModules.publicHoistPattern == null) {
     delete saveModules.publicHoistPattern
   }
+  if (!saveModules.virtualStoreOnly) {
+    delete saveModules.virtualStoreOnly
+  }
   if ((saveModules.hoistedAliases == null) || (saveModules.hoistPattern == null) && (saveModules.publicHoistPattern == null)) {
     delete saveModules.hoistedAliases
   }