Resolve "Fix Geo::RepositoriesCleanUpWorker to work with hashed storage"

What does this MR do?

Fix Geo::RepositoriesCleanUpWorker to work with hashed storage.

Why was this MR needed?

Repositories backed by hashed storage got stale on the file system when repositories selected for selective replication have changed.

Does this MR meet the acceptance criteria?

• Changelog entry added, if necessary
• Documentation created/updated
• API support added
• Tests added for this feature/bug
• Review
  • Has been reviewed by UX
  • Has been reviewed by Frontend
  • Has been reviewed by Backend
  • Has been reviewed by Database
• Conform by the merge request performance guides
• Conform by the style guides
• Squashed related commits together
• Internationalization required/considered
• If paid feature, have we considered GitLab.com plan and how it works for groups and is there a design for promoting it to users who aren't on the correct plan

What are the relevant issue numbers?

Closes #4596 (closed)