fix: peer dependency is not unlinked when adding a new dependency (#6274)

close #6272

.changeset/real-eels-approve.md

@@ -0,0 +1,6 @@
+---
+"@pnpm/resolve-dependencies": patch
+"pnpm": patch
+---
+
+Peer dependency is not unlinked when adding a new dependency [#6272](https://github.com/pnpm/pnpm/issues/6272).

pkg-manager/resolve-dependencies/src/index.ts

@@ -178,9 +178,12 @@ export async function resolveDependencies (
       ? await getTopParents(
         difference(
           Object.keys(getAllDependenciesFromManifest(project.manifest)),
-          resolvedImporter.directDependencies
-            .filter((dep, index) => project.wantedDependencies[index]?.isNew === true)
-            .map(({ alias }) => alias) || []
+          [
+            ...resolvedImporter.directDependencies
+              .filter((_, index) => project.wantedDependencies[index]?.isNew === true)
+              .map(({ alias }) => alias) || [],
+            ...resolvedImporter.linkedDependencies.map(({ alias }) => alias),
+          ]
         ),
         project.modulesDir
       )

pnpm/test/monorepo/peerDependencies.ts

@@ -0,0 +1,35 @@
+import { promises as fs } from 'fs'
+import { WANTED_LOCKFILE } from '@pnpm/constants'
+import type { Lockfile } from '@pnpm/lockfile-types'
+import { preparePackages } from '@pnpm/prepare'
+import readYamlFile from 'read-yaml-file'
+import writeYamlFile from 'write-yaml-file'
+import { execPnpm } from '../utils'
+
+// Covers https://github.com/pnpm/pnpm/issues/6272
+test('peer dependency is not unlinked when adding a new dependency', async () => {
+  preparePackages([
+    {
+      name: 'project-1',
+
+      dependencies: {
+        '@pnpm.e2e/abc': '1.0.0',
+        '@pnpm.e2e/peer-a': 'workspace:*',
+      },
+    },
+    {
+      name: '@pnpm.e2e/peer-a',
+      version: '1.0.0',
+
+      dependencies: {},
+    },
+  ])
+
+  await fs.writeFile('.npmrc', 'auto-install-peers=false', 'utf8')
+  await writeYamlFile('pnpm-workspace.yaml', { packages: ['**', '!store/**'] })
+  await execPnpm(['install'])
+  await execPnpm(['--filter=project-1', 'add', 'is-odd@1.0.0'])
+
+  const lockfile = await readYamlFile<Lockfile>(WANTED_LOCKFILE)
+  expect(Object.keys(lockfile!.packages!)).toContain('/@pnpm.e2e/abc@1.0.0(@pnpm.e2e/peer-a@@pnpm.e2e+peer-a)')
+})