fix: don't remove hoisted dependencies from .pnpm on repeat install (#5971)

.changeset/rare-dragons-crash.md

@@ -0,0 +1,7 @@
+---
+"@pnpm/modules-cleaner": patch
+"@pnpm/core": patch
+"pnpm": patch
+---
+
+Packages hoisted to the virtual store are not removed on repeat install, when the non-headless algorithm runs the installation.

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

@@ -245,7 +245,9 @@ export async function linkPackages (
   }
 
   let newHoistedDependencies!: HoistedDependencies
-  if ((opts.hoistPattern != null || opts.publicHoistPattern != null) && (newDepPaths.length > 0 || removedDepPaths.size > 0)) {
+  if (opts.hoistPattern == null && opts.publicHoistPattern == null) {
+    newHoistedDependencies = {}
+  } else if (newDepPaths.length > 0 || removedDepPaths.size > 0) {
     // It is important to keep the skipped packages in the lockfile which will be saved as the "current lockfile".
     // pnpm is comparing the current lockfile to the wanted one and they should match.
     // But for hoisting, we need a version of the lockfile w/o the skipped packages, so we're making a copy.
@@ -264,7 +266,7 @@ export async function linkPackages (
       virtualStoreDir: opts.virtualStoreDir,
     })
   } else {
-    newHoistedDependencies = {}
+    newHoistedDependencies = opts.hoistedDependencies
   }
 
   return {

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

@@ -20,7 +20,7 @@ import { testDefaults } from '../utils'
 test('should hoist dependencies', async () => {
   const project = prepareEmpty()
 
-  await addDependenciesToPackage({}, ['express', '@foo/has-dep-from-same-scope'], await testDefaults({ fastUnpack: false, hoistPattern: '*' }))
+  const manifest = await addDependenciesToPackage({}, ['express', '@foo/has-dep-from-same-scope'], await testDefaults({ fastUnpack: false, hoistPattern: '*' }))
 
   await project.has('express')
   await project.has('.pnpm/node_modules/debug')
@@ -31,6 +31,19 @@ test('should hoist dependencies', async () => {
 
   // should also hoist bins
   await project.isExecutable('.pnpm/node_modules/.bin/mime')
+
+  const modules = await project.readModulesManifest()
+  expect(Object.keys(modules!.hoistedDependencies).length > 0).toBeTruthy()
+
+  // On repeat install the hoisted packages are preserved (non-headless install)
+  await install(manifest, await testDefaults({ fastUnpack: false, hoistPattern: '*', preferFrozenLockfile: false, modulesCacheMaxAge: 0 }))
+  await project.has('.pnpm/node_modules/debug')
+  expect((await project.readModulesManifest())!.hoistedDependencies).toStrictEqual(modules!.hoistedDependencies)
+
+  // On repeat install the hoisted packages are preserved (headless install)
+  await install(manifest, await testDefaults({ fastUnpack: false, hoistPattern: '*', frozenLockfile: true, modulesCacheMaxAge: 0 }))
+  await project.has('.pnpm/node_modules/debug')
+  expect((await project.readModulesManifest())!.hoistedDependencies).toStrictEqual(modules!.hoistedDependencies)
 })
 
 test('should hoist dependencies to the root of node_modules when publicHoistPattern is used', async () => {

pkg-manager/modules-cleaner/src/prune.ts

@@ -156,7 +156,7 @@ export async function prune (
           .map((orphanDepPath) => depPathToFilename(orphanDepPath))
           .map(async (orphanDepPath) => _tryRemovePkg(orphanDepPath))
       )
-      const neededPkgs: Set<string> = new Set()
+      const neededPkgs: Set<string> = new Set(['node_modules'])
       for (const depPath of Object.keys(opts.wantedLockfile.packages ?? {})) {
         if (opts.skipped.has(depPath)) continue
         neededPkgs.add(depPathToFilename(depPath))