fix(arborist): clean up stale .store and hoisted dirs on strategy switch (#9647)

In continuation of our exploration of using `install-strategy=linked` in
the [Gutenberg
monorepo](https://github.com/WordPress/gutenberg/pull/75814), 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