fix: Preserve Bun prune lockfile validity (#12686)
## Summary
- Preserve Bun lockfile entries needed by the copied root workspace and
de-aliased nested resolutions so pruned outputs remain
frozen-installable.
- Add the public #12653 Bun reproduction to `check-lockfiles`, pinned to
the failing `@eventmate/migrations` prune target.
- Fixes #12653
