Make Gitlab::Git::Repository#run_git private

What does this MR do?

Makes Gitlab::Git::Repository#run_git a private method.

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

Why was this MR needed?

Limit where we can shell out to git. Eventually only Gitaly can do that.

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

What are the relevant issue numbers?