Find and mark more Git disk access locations, part 2

What does this MR do?

Follow-up to https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/19363

This marks a few more places in our code with 'allow disk access' blocks in preparation for making it an exception to directly access Git repositories.

While working on this I ended up moving some code, which then prompted me to change how we handle Git hooks during tests. Instead of trying to delete them from every repo the tests create, I made it so that the gitlab-shell hooks in tmp/tests/gitlab-shell/hooks are no-ops that always pass.

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
• Conform by the merge request performance guides
• Conform by the style guides
• If you have multiple commits, please combine them into a few logically organized commits by squashing them
• Internationalization required/considered
• End-to-end tests pass (package-and-qa manual pipeline job)

What are the relevant issue numbers?