fix: don't overwrite node_modules inside inject dependencies

.changeset/hip-actors-boil.md

@@ -0,0 +1,6 @@
+---
+"@pnpm/lifecycle": patch
+"pnpm": patch
+---
+
+`node_modules` directories inside injected dependencies should not be overwritten.

packages/core/test/install/injectLocalPackages.ts

@@ -357,8 +357,6 @@ test('inject local packages when node-linker is hoisted', async () => {
     version: '1.0.0',
     dependencies: {
       'is-negative': '1.0.0',
-    },
-    devDependencies: {
       'dep-of-pkg-with-1-dep': '100.0.0',
     },
     peerDependencies: {
@@ -370,6 +368,7 @@ test('inject local packages when node-linker is hoisted', async () => {
     version: '1.0.0',
     dependencies: {
       'project-1': 'workspace:1.0.0',
+      'dep-of-pkg-with-1-dep': '101.0.0',
     },
     devDependencies: {
       'is-positive': '1.0.0',
@@ -461,6 +460,7 @@ test('inject local packages when node-linker is hoisted', async () => {
   await rootModules.has('is-positive')
 
   await projects['project-2'].has('project-1')
+  await projects['project-2'].has('project-1/node_modules/dep-of-pkg-with-1-dep')
 
   await projects['project-3'].has('project-1')
   await projects['project-3'].has('project-2')
@@ -485,6 +485,7 @@ test('inject local packages when node-linker is hoisted', async () => {
         'is-positive': '>=1.0.0',
       },
       dependencies: {
+        'dep-of-pkg-with-1-dep': '100.0.0',
         'is-negative': '1.0.0',
         'is-positive': '1.0.0',
       },
@@ -499,6 +500,7 @@ test('inject local packages when node-linker is hoisted', async () => {
       name: 'project-2',
       version: '1.0.0',
       dependencies: {
+        'dep-of-pkg-with-1-dep': '101.0.0',
         'project-1': 'file:project-1_is-positive@2.0.0',
       },
       transitivePeerDependencies: ['is-positive'],

packages/lifecycle/src/runLifecycleHooksConcurrently.ts

@@ -1,3 +1,5 @@
+import fs from 'fs'
+import path from 'path'
 import { fetchFromDir } from '@pnpm/directory-fetcher'
 import { StoreController } from '@pnpm/store-controller-types'
 import { ProjectManifest } from '@pnpm/types'
@@ -53,16 +55,46 @@ export default async function runLifecycleHooksConcurrently (
         if (targetDirs == null || targetDirs.length === 0) return
         const filesResponse = await fetchFromDir(rootDir, {})
         await Promise.all(
-          targetDirs.map((targetDir) => opts.storeController.importPackage(targetDir, {
-            filesResponse: {
-              fromStore: false,
-              ...filesResponse,
-            },
-            force: false,
-          }))
+          targetDirs.map(async (targetDir) => {
+            const targetModulesDir = path.join(targetDir, 'node_modules')
+            const nodeModulesIndex = {}
+            if (fs.existsSync(targetModulesDir)) {
+              // If the target directory contains a node_modules directory
+              // (it may happen when the hoisted node linker is used)
+              // then we need to preserve this node_modules.
+              // So we scan this node_modules directory and  pass it as part of the new package.
+              await scanDir('node_modules', targetModulesDir, targetModulesDir, nodeModulesIndex)
+            }
+            return opts.storeController.importPackage(targetDir, {
+              filesResponse: {
+                fromStore: false,
+                ...filesResponse,
+                filesIndex: {
+                  ...filesResponse.filesIndex,
+                  ...nodeModulesIndex,
+                },
+              },
+              force: false,
+            })
+          })
         )
       }
     )
   })
   await runGroups(childConcurrency, groups)
 }
+
+async function scanDir (prefix: string, rootDir: string, currentDir: string, index: Record<string, string>) {
+  const files = await fs.promises.readdir(currentDir)
+  await Promise.all(files.map(async (file) => {
+    const fullPath = path.join(currentDir, file)
+    const stat = await fs.promises.stat(fullPath)
+    if (stat.isDirectory()) {
+      return scanDir(prefix, rootDir, fullPath, index)
+    }
+    if (stat.isFile()) {
+      const relativePath = path.relative(rootDir, fullPath)
+      index[path.join(prefix, relativePath)] = fullPath
+    }
+  }))
+}