Remove Gitlab::Git::Repository#rugged

What does this MR do?

Remove the Gitlab::Git::Repository#rugged method, cleanup code, and refactor tests that still use Rugged. After this, there should be no Rugged code that access the instance's repositories on non-test environments. There is still some rugged code for other tasks like the repository import task, but since it doesn't access any repository storage path it can stay.

What are the relevant issue numbers?

Part of gitaly#1280 (closed)

Does this MR meet the acceptance criteria?

• Changelog entry added, if necessary
• Documentation created/updated
• Tests added for this feature/bug
• Conforms to the code review guidelines
• Conforms to the merge request performance guidelines
• Conforms to the style guides
• Conforms to the database guides