Use gitaly to set/unset git config

What does this MR do?

Migrates a use of rugged.config to use Gitaly instead.

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
• Conform by the code review guidelines
  • Has been reviewed by a UX Designer
  • Has been reviewed by a Frontend maintainer
  • Has been reviewed by a Backend maintainer
  • Has been reviewed by a Database specialist
• EE specific content should be in the top level /ee folder
• Conform by the merge request performance guides
• Conform by the style guides
• Conform by the database guides
• If you have multiple commits, please combine them into a few logically organized commits by squashing them
• 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-and-qa manual pipeline job)

What are the relevant issue numbers?

Closes gitaly#1241 (closed)