Wrap Rugged-exceptions in Gitlab::Git::Repository#write_ref

Why?

When we migrate things to Gitaly, we shouldn't have handle Rugged::*Exception in app/models/.

Also moved shell_write_ref and rugged_write_ref into private

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?

gitaly#784 (closed)

/cc @jacobvosmaer-gitlab