feat: enable injected local packages to work with global virtual store (#10366)

* feat: enable injected local packages to work with global virtual store

by leveraging `pkgLocationsByDepPath` for `file:` dependencies.

* fix: populate `pkgLocationsByDepPath` directly for directory dependencies in the graph builder

* refactor: store directory dependencies as a Map instead of an object

* refactor: improve file: dependency target directory resolution

by prioritizing `directoryDepsByDepPath` and providing a lockfile fallback.

* refactor: remove `pkgLocationsByDepPath` from hoisted dependency graph generation parameters

* test: fix

* test: fix

* refactor: simplify directory lookup for injected workspace packages

by directly using the dependency graph

* refactor: move extendProjectsWithTargetDirs to headless module and update imports

* refactor: make `directoryDepsByDepPath` required

in `LockfileToDepGraphOptions` and remove its nullish coalescing in headless

* refactor: directory dependency tracking

by renaming `directoryDepsByDepPath` to `injectionTargetsByDepPath`
and extracting related logic, and remove an unused export.

* docs: add changesets

* fix: implemented CR suggestions

.changeset/brave-bears-worry.md

@@ -0,0 +1,5 @@
+---
+"@pnpm/headless": minor
+---
+
+Export extendProjectsWithTargetDirs.

.changeset/fix-injected-deps-global-vstore.md

@@ -0,0 +1,9 @@
+---
+"@pnpm/deps.graph-builder": patch
+"@pnpm/headless": patch
+"@pnpm/core": patch
+---
+
+Fixed injected local packages to work correctly with the global virtual store [#10366](https://github.com/pnpm/pnpm/pull/10366).
+
+When using `nodeLinker: 'isolated'` with `enableGlobalVirtualStore: true`, injected workspace packages now use the correct hash-based paths from the global virtual store instead of project-relative paths.

.changeset/spotty-gifts-chew.md

@@ -0,0 +1,5 @@
+---
+"@pnpm/lockfile.utils": major
+---
+
+Remove extendProjectsWithTargetDirs.

deps/graph-builder/src/lockfileToDepGraph.ts

@@ -99,7 +99,7 @@ export interface LockfileToDepGraphResult {
   hoistedLocations?: Record<string, string[]>
   symlinkedDirectDependenciesByImporterId?: DirectDependenciesByImporterId
   prevGraph?: DependenciesGraph
-  pkgLocationsByDepPath?: Record<string, string[]>
+  injectionTargetsByDepPath: Map<string, string[]>
 }
 
 /**
@@ -119,6 +119,7 @@ export async function lockfileToDepGraph (
   const {
     graph,
     locationByDepPath,
+    injectionTargetsByDepPath,
   } = await buildGraphFromPackages(lockfile, currentLockfile, opts)
 
   const _getChildrenPaths = getChildrenPaths.bind(null, {
@@ -156,7 +157,7 @@ export async function lockfileToDepGraph (
     directDependenciesByImporterId[importerId] = _getChildrenPaths(rootDeps, null, importerId)
   }
 
-  return { graph, directDependenciesByImporterId }
+  return { graph, directDependenciesByImporterId, injectionTargetsByDepPath }
 }
 
 async function buildGraphFromPackages (
@@ -166,10 +167,13 @@ async function buildGraphFromPackages (
 ): Promise<{
     graph: DependenciesGraph
     locationByDepPath: Record<string, string>
+    injectionTargetsByDepPath: Map<string, string[]>
   }> {
   const currentPackages = currentLockfile?.packages ?? {}
   const graph: DependenciesGraph = {}
   const locationByDepPath: Record<string, string> = {}
+  // Only populated for directory deps (injected workspace packages)
+  const injectionTargetsByDepPath = new Map<string, string[]>()
 
   const _getPatchInfo = getPatchInfo.bind(null, opts.patchedDependencies)
   const promises: Array<Promise<void>> = []
@@ -201,7 +205,8 @@ async function buildGraphFromPackages (
         return
       }
 
-      const depIsPresent = !('directory' in pkgSnapshot.resolution && pkgSnapshot.resolution.directory != null) &&
+      const isDirectoryDep = 'directory' in pkgSnapshot.resolution && pkgSnapshot.resolution.directory != null
+      const depIsPresent = !isDirectoryDep &&
         currentPackages[depPath] &&
         equals(currentPackages[depPath].dependencies, pkgSnapshot.dependencies)
 
@@ -210,6 +215,10 @@ async function buildGraphFromPackages (
       const modules = path.join(opts.virtualStoreDir, dirNameInVirtualStore, 'node_modules')
       const dir = path.join(modules, pkgName)
       locationByDepPath[depPath] = dir
+      // Track directory deps for injected workspace packages
+      if (isDirectoryDep) {
+        injectionTargetsByDepPath.set(depPath, [dir])
+      }
 
       let dirExists: boolean | undefined
       if (
@@ -273,7 +282,7 @@ async function buildGraphFromPackages (
     })())
   }
   await Promise.all(promises)
-  return { graph, locationByDepPath }
+  return { graph, locationByDepPath, injectionTargetsByDepPath }
 }
 
 interface GetChildrenPathsContext {

lockfile/utils/src/extendProjectsWithTargetDirs.ts

@@ -1,36 +0,0 @@
-import path from 'path'
-import { type LockfileObject, type TarballResolution } from '@pnpm/lockfile.types'
-import { depPathToFilename } from '@pnpm/dependency-path'
-import { type ProjectId, type DepPath } from '@pnpm/types'
-import { packageIdFromSnapshot } from './packageIdFromSnapshot.js'
-import { nameVerFromPkgSnapshot } from './nameVerFromPkgSnapshot.js'
-
-type GetLocalLocations = (depPath: DepPath, pkgName: string) => string[]
-
-export function extendProjectsWithTargetDirs<T> (
-  projects: Array<T & { id: ProjectId }>,
-  lockfile: LockfileObject,
-  ctx: {
-    virtualStoreDir: string
-    pkgLocationsByDepPath?: Record<DepPath, string[]>
-    virtualStoreDirMaxLength: number
-  }
-): Array<T & { id: ProjectId, stages: string[], targetDirs: string[] }> {
-  const getLocalLocations: GetLocalLocations = ctx.pkgLocationsByDepPath != null
-    ? (depPath: DepPath) => ctx.pkgLocationsByDepPath![depPath]
-    : (depPath: DepPath, pkgName: string) => [path.join(ctx.virtualStoreDir, depPathToFilename(depPath, ctx.virtualStoreDirMaxLength), 'node_modules', pkgName)]
-  const projectsById: Record<ProjectId, T & { id: ProjectId, targetDirs: string[], stages?: string[] }> =
-    Object.fromEntries(projects.map((project) => [project.id, { ...project, targetDirs: [] as string[] }]))
-  for (const [depPath, pkg] of Object.entries(lockfile.packages ?? {})) {
-    if ((pkg.resolution as TarballResolution)?.type !== 'directory') continue
-    const pkgId = packageIdFromSnapshot(depPath as DepPath, pkg)
-    const { name: pkgName } = nameVerFromPkgSnapshot(depPath, pkg)
-    const importerId = pkgId.replace(/^file:/, '') as ProjectId
-    if (projectsById[importerId] == null) continue
-    const localLocations = getLocalLocations(depPath as DepPath, pkgName)
-    if (!localLocations) continue
-    projectsById[importerId].targetDirs.push(...localLocations)
-    projectsById[importerId].stages = ['preinstall', 'install', 'postinstall', 'prepare', 'prepublishOnly']
-  }
-  return Object.values(projectsById) as Array<T & { id: ProjectId, stages: string[], targetDirs: string[] }>
-}

lockfile/utils/src/index.ts

@@ -1,6 +1,5 @@
 import { refToRelative } from '@pnpm/dependency-path'
 
-export { extendProjectsWithTargetDirs } from './extendProjectsWithTargetDirs.js'
 export { nameVerFromPkgSnapshot } from './nameVerFromPkgSnapshot.js'
 export { packageIdFromSnapshot } from './packageIdFromSnapshot.js'
 export { packageIsIndependent } from './packageIsIndependent.js'

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

@@ -25,7 +25,7 @@ import {
 } from '@pnpm/lockfile.settings-checker'
 import { PnpmError } from '@pnpm/error'
 import { getContext, type PnpmContext } from '@pnpm/get-context'
-import { headlessInstall, type InstallationResultStats } from '@pnpm/headless'
+import { extendProjectsWithTargetDirs, headlessInstall, type InstallationResultStats } from '@pnpm/headless'
 import {
   makeNodeRequireOption,
   runLifecycleHook,
@@ -43,7 +43,6 @@ import {
   type CatalogSnapshots,
 } from '@pnpm/lockfile.fs'
 import { writePnpFile } from '@pnpm/lockfile-to-pnp'
-import { extendProjectsWithTargetDirs } from '@pnpm/lockfile.utils'
 import { allProjectsAreUpToDate, satisfiesPackageManifest } from '@pnpm/lockfile.verification'
 import { getPreferredVersionsFromLockfileAndManifests } from '@pnpm/lockfile.preferred-versions'
 import { logger, globalInfo, streamParser } from '@pnpm/logger'
@@ -1471,10 +1470,7 @@ const _installInContext: InstallFunction = async (projects, ctx, opts) => {
       }
     }))
 
-    const projectsWithTargetDirs = extendProjectsWithTargetDirs(projects, newLockfile, {
-      virtualStoreDir: ctx.virtualStoreDir,
-      virtualStoreDirMaxLength: opts.virtualStoreDirMaxLength,
-    })
+    const projectsWithTargetDirs = getProjectsWithTargetDirs(projects, newLockfile, dependenciesGraph)
     const currentLockfileDir = path.join(ctx.rootModulesDir, '.pnpm')
     await Promise.all([
       opts.useLockfile && opts.saveLockfile
@@ -1732,3 +1728,28 @@ export class IgnoredBuildsError extends PnpmError {
 function dedupePackageNamesFromIgnoredBuilds (ignoredBuilds: IgnoredBuilds): string[] {
   return Array.from(new Set(Array.from(ignoredBuilds ?? []).map(dp.removeSuffix))).sort(lexCompare)
 }
+
+/**
+ * Build injectionTargetsByDepPath from the dependenciesGraph for injected workspace packages
+ * and extend projects with their target directories.
+ * The dependenciesGraph already has the correct `dir` values after `extendGraph` is applied
+ * (which uses the correct hash-based paths when global virtual store is enabled).
+ */
+function getProjectsWithTargetDirs<T extends { id: ProjectId }> (
+  projects: T[],
+  lockfile: LockfileObject,
+  dependenciesGraph: DependenciesGraph
+): Array<T & { id: ProjectId, stages: string[], targetDirs: string[] }> {
+  const injectionTargetsByDepPath = new Map<string, string[]>()
+  if (lockfile.packages) {
+    for (const [depPath, { resolution }] of Object.entries(lockfile.packages)) {
+      if (resolution?.type === 'directory') {
+        const graphNode = dependenciesGraph[depPath as DepPath]
+        if (graphNode?.dir) {
+          injectionTargetsByDepPath.set(depPath, [graphNode.dir])
+        }
+      }
+    }
+  }
+  return extendProjectsWithTargetDirs(projects, injectionTargetsByDepPath)
+}

pkg-manager/core/test/install/globalVirtualStore.ts

@@ -1,7 +1,9 @@
 import fs from 'fs'
 import path from 'path'
-import { prepareEmpty } from '@pnpm/prepare'
-import { install } from '@pnpm/core'
+import { assertProject } from '@pnpm/assert-project'
+import { prepareEmpty, preparePackages } from '@pnpm/prepare'
+import { install, type MutatedProject, mutateModules, type ProjectOptions } from '@pnpm/core'
+import { type ProjectRootDir } from '@pnpm/types'
 import { sync as rimraf } from '@zkochan/rimraf'
 import { testDefaults } from '../utils/index.js'
 
@@ -71,3 +73,81 @@ test('modules are correctly updated when using a global virtual store', async ()
     expect(fs.existsSync(path.join(globalVirtualStoreDir, '@pnpm.e2e/peer-c/2.0.0', files[0], 'node_modules/@pnpm.e2e/peer-c/package.json'))).toBeTruthy()
   }
 })
+
+test('injected local packages work with global virtual store', async () => {
+  const project1Manifest = {
+    name: 'project-1',
+    version: '1.0.0',
+    dependencies: {
+      'is-positive': '1.0.0',
+    },
+  }
+  const project2Manifest = {
+    name: 'project-2',
+    version: '1.0.0',
+    dependencies: {
+      'project-1': 'workspace:1.0.0',
+    },
+    dependenciesMeta: {
+      'project-1': {
+        injected: true,
+      },
+    },
+  }
+  preparePackages([
+    {
+      location: 'project-1',
+      package: project1Manifest,
+    },
+    {
+      location: 'project-2',
+      package: project2Manifest,
+    },
+  ])
+  fs.writeFileSync('project-1/foo.js', '', 'utf8')
+
+  const globalVirtualStoreDir = path.resolve('links')
+  const importers: MutatedProject[] = [
+    {
+      mutation: 'install',
+      rootDir: path.resolve('project-1') as ProjectRootDir,
+    },
+    {
+      mutation: 'install',
+      rootDir: path.resolve('project-2') as ProjectRootDir,
+    },
+  ]
+  const allProjects: ProjectOptions[] = [
+    {
+      buildIndex: 0,
+      manifest: project1Manifest,
+      rootDir: path.resolve('project-1') as ProjectRootDir,
+    },
+    {
+      buildIndex: 0,
+      manifest: project2Manifest,
+      rootDir: path.resolve('project-2') as ProjectRootDir,
+    },
+  ]
+
+  await mutateModules(importers, testDefaults({
+    autoInstallPeers: false,
+    allProjects,
+    enableGlobalVirtualStore: true,
+    dedupeInjectedDeps: false,
+    virtualStoreDir: globalVirtualStoreDir,
+  }))
+
+  // Verify project-2 has project-1 installed
+  expect(fs.existsSync(path.resolve('project-2/node_modules/project-1'))).toBeTruthy()
+
+  // Verify the modules manifest has injectedDeps pointing to global virtual store
+  const rootModules = assertProject(process.cwd())
+  const modulesState = rootModules.readModulesManifest()
+  expect(modulesState?.injectedDeps?.['project-1']).toBeDefined()
+  expect(modulesState?.injectedDeps?.['project-1'].length).toBeGreaterThan(0)
+  // Injected deps should be in the global virtual store (links directory)
+  const injectedDepLocation = modulesState?.injectedDeps?.['project-1'][0]
+  expect(injectedDepLocation).toContain('links')
+  expect(fs.existsSync(path.join(injectedDepLocation!, 'foo.js'))).toBeTruthy()
+})

pkg-manager/headless/src/extendProjectsWithTargetDirs.ts

@@ -0,0 +1,26 @@
+import { parse as parseDepPath } from '@pnpm/dependency-path'
+import { type ProjectId } from '@pnpm/types'
+
+export function extendProjectsWithTargetDirs<T> (
+  projects: Array<T & { id: ProjectId }>,
+  injectionTargetsByDepPath: Map<string, string[]>
+): Array<T & { id: ProjectId, stages: string[], targetDirs: string[] }> {
+  const projectsById: Record<ProjectId, T & { id: ProjectId, targetDirs: string[], stages?: string[] }> =
+        Object.fromEntries(projects.map((project) => [project.id, { ...project, targetDirs: [] as string[] }]))
+
+  for (const [depPath, locations] of injectionTargetsByDepPath) {
+    const parsed = parseDepPath(depPath)
+    if (!parsed.name || !parsed.nonSemverVersion?.startsWith('file:')) continue
+    const importerId = parsed.nonSemverVersion.replace(/^file:/, '') as ProjectId
+    if (projectsById[importerId] == null) continue
+    // Dedupe: only add locations that aren't already tracked
+    for (const location of locations) {
+      if (!projectsById[importerId].targetDirs.includes(location)) {
+        projectsById[importerId].targetDirs.push(location)
+      }
+    }
+    projectsById[importerId].stages = ['preinstall', 'install', 'postinstall', 'prepare', 'prepublishOnly']
+  }
+
+  return Object.values(projectsById) as Array<T & { id: ProjectId, stages: string[], targetDirs: string[] }>
+}

pkg-manager/headless/src/index.ts

@@ -34,9 +34,9 @@ import {
 } from '@pnpm/lockfile.fs'
 import { writePnpFile } from '@pnpm/lockfile-to-pnp'
 import {
-  extendProjectsWithTargetDirs,
   nameVerFromPkgSnapshot,
 } from '@pnpm/lockfile.utils'
+import { extendProjectsWithTargetDirs } from './extendProjectsWithTargetDirs.js'
 import {
   type LogBase,
   logger,
@@ -92,6 +92,7 @@ import {
 } from '@pnpm/deps.graph-builder'
 import { lockfileToHoistedDepGraph } from './lockfileToHoistedDepGraph.js'
 import { linkDirectDeps, type LinkedDirectDep } from '@pnpm/pkg-manager.direct-dep-linker'
+export { extendProjectsWithTargetDirs } from './extendProjectsWithTargetDirs.js'
 
 export type { HoistingLimits }
 
@@ -344,7 +345,7 @@ export async function headlessInstall (opts: HeadlessOptions): Promise<Installat
     graph,
     hierarchy,
     hoistedLocations,
-    pkgLocationsByDepPath,
+    injectionTargetsByDepPath,
     prevGraph,
     symlinkedDirectDependenciesByImporterId,
   } = await (
@@ -574,11 +575,7 @@ export async function headlessInstall (opts: HeadlessOptions): Promise<Installat
     }
   }
 
-  const projectsToBeBuilt = extendProjectsWithTargetDirs(selectedProjects, wantedLockfile, {
-    pkgLocationsByDepPath,
-    virtualStoreDir,
-    virtualStoreDirMaxLength: opts.virtualStoreDirMaxLength,
-  })
+  const projectsToBeBuilt = extendProjectsWithTargetDirs(selectedProjects, injectionTargetsByDepPath)
 
   if (opts.enableModulesDir !== false) {
     const rootProjectDeps = !opts.dedupeDirectDeps ? {} : (directDependenciesByImporterId['.'] ?? {})

pkg-manager/headless/src/lockfileToHoistedDepGraph.ts

@@ -89,7 +89,8 @@ async function _lockfileToHoistedDepGraph (
     ...opts,
     lockfile,
     graph,
-    pkgLocationsByDepPath: {},
+    pkgLocationsByDepPath: {} as Record<string, string[]>,
+    injectionTargetsByDepPath: new Map<string, string[]>(),
     hoistedLocations: {} as Record<string, string[]>,
   }
   const hierarchy = {
@@ -120,9 +121,9 @@ async function _lockfileToHoistedDepGraph (
     directDependenciesByImporterId,
     graph,
     hierarchy,
-    pkgLocationsByDepPath: fetchDepsOpts.pkgLocationsByDepPath,
     symlinkedDirectDependenciesByImporterId,
     hoistedLocations: fetchDepsOpts.hoistedLocations,
+    injectionTargetsByDepPath: fetchDepsOpts.injectionTargetsByDepPath,
   }
 }
 
@@ -159,6 +160,7 @@ async function fetchDeps (
     graph: DependenciesGraph
     lockfile: LockfileObject
     pkgLocationsByDepPath: Record<string, string[]>
+    injectionTargetsByDepPath: Map<string, string[]>
     hoistedLocations: Record<string, string[]>
   } & LockfileToHoistedDepGraphOptions,
   modules: string,
@@ -261,6 +263,15 @@ async function fetchDeps (
       opts.pkgLocationsByDepPath[depPath] = []
     }
     opts.pkgLocationsByDepPath[depPath].push(dir)
+    // Track directory deps for injected workspace packages
+    if ('directory' in pkgSnapshot.resolution && pkgSnapshot.resolution.directory != null) {
+      const locations = opts.injectionTargetsByDepPath.get(depPath)
+      if (locations) {
+        locations.push(dir)
+      } else {
+        opts.injectionTargetsByDepPath.set(depPath, [dir])
+      }
+    }
     depHierarchy[dir] = await fetchDeps(opts, path.join(dir, 'node_modules'), dep.dependencies)
     if (!opts.hoistedLocations[depPath]) {
       opts.hoistedLocations[depPath] = []