fix: don't always index the project directory (#3964)

close #3949

.changeset/honest-cougars-marry.md

@@ -0,0 +1,6 @@
+---
+"@pnpm/lifecycle": patch
+"pnpm": patch
+---
+
+Do not index the project directory if it should not be hard linked to any other project [#3949](https://github.com/pnpm/pnpm/issues/3949).

packages/lifecycle/src/runLifecycleHooksConcurrently.ts

@@ -50,7 +50,7 @@ export default async function runLifecycleHooksConcurrently (
           if ((manifest.scripts == null) || !manifest.scripts[stage]) continue
           await runLifecycleHook(stage, manifest, runLifecycleHookOpts)
         }
-        if (targetDirs == null) return
+        if (targetDirs == null || targetDirs.length === 0) return
         const filesResponse = await fetchFromDir(rootDir, {})
         await Promise.all(
           targetDirs.map((targetDir) => opts.storeController.importPackage(targetDir, {