Migrate merge base, merged branches, write ref

What does this MR do?

Removes the following Gitaly feature flags: gitaly_merge_base, gitaly_merged_branch_names, gitaly_write_ref.

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 to 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
• Conforms to the merge request performance guidelines
• Conforms to the style guides
• Conform to the database 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?

Closes gitaly#748 (closed), gitaly#695 (closed), gitaly#799 (closed)