Remove some Rugged dependencies from Repository

What does this MR do?

Pushes some EE-only code that calls Rugged out of the Repository class.

Are there points in the code the reviewer needs to double check?

Why was this MR needed?

Screenshots (if relevant)

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
• End-to-end tests pass (package-qa manual pipeline job)

What are the relevant issue numbers?