Remove some easy cases of 'path_to_repo' use

What does this MR do?

This moves and removes some easy cases where we use Repository#path_to_repo. With Gitaly, this attribute will disappear from the application, so we need to get rid of it in the code.

Also adds some comments referring to Gitaly issues.

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

What are the relevant issue numbers?