When the database has orphaned foreign key references (dependencies or labels
pointing to non-existent issues), the migration invariant check would fail,
preventing the database from opening. This created a chicken-and-egg problem:
1. bd doctor --fix tries to open the database
2. Opening triggers migrations with invariant checks
3. Invariant check fails due to orphaned refs
4. Fix never runs because database won't open
The fix adds CleanOrphanedRefs() that runs BEFORE captureSnapshot() in
RunMigrations. This automatically cleans up orphaned dependencies and labels
(preserving external:* refs), allowing the database to open normally.
Added test coverage for the cleanup function.
