fix(arborist): clean up stale .store and hoisted dirs on strategy switch

[manzoorwanijk]

In continuation of our exploration of using install-strategy=linked in the Gutenberg monorepo, which powers the WordPress Block Editor.

Switching install-strategy in the same project directory left behind the previous strategy's layout. Going hoisted → linked kept the stale real top-level transitive directories alongside the new .store/ and symlinks; going linked → hoisted kept the entire node_modules/.store/ directory. A fresh install of either strategy was already clean — only the switch was affected.

Why

Under the linked strategy the actual tree the diff compares against is synthesized from the ideal tree (#buildLinkedActualForDiff), so real directories left over from a prior hoisted layout are never seen, and #cleanOrphanedTopLevelLinks only removed symlinks. In the other direction load-actual ignores dot-directories, so the hoisted diff never sees node_modules/.store and never removes it.

How

reify.js now removes the leftover .store on a non-linked reify via #removeStaleStoreDir. The store lives only at the project root and is exclusively a linked artifact, so a single removal covers the project. It runs only for a full-project install — a workspace-filtered or --workspaces=false install is skipped, because out-of-scope workspaces may still link into the store.

#cleanOrphanedTopLevelLinks (run only under linked) additionally removes stale real package directories — a directory containing a package.json that is not in the ideal tree's valid top-level set — and prunes an emptied @scope directory afterward. Non-package real directories and symlinks pointing outside the project are still preserved.

The valid-top-level collection in #cleanOrphanedStoreEntries no longer skips non-link nodes, so the root's bundled dependencies — materialized as real top-level directories under linked — are recorded as valid and never swept as stale.

References

Fixes #9615
Part of #9608

[github-actions]

🎉 Backport to release/v11 created: #9649