Geo: Mark missing primary files as synced, and add logging and metrics for sysadmins to investigate missing files

What does this MR do?

• When a secondary attempts to download from the primary and receives "file not found" as opposed to "record not found", mark the file as synced
• Resync files that are marked synced but missing on the primary. Same low priority as retrying failures.
• Add sufficient logging and metrics for sysadmins to be able to investigate files missing on the primary

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

Why was this MR needed?

Files missing on the primary inflate the sync failure counts, but are not recoverable. From the perspective of the secondary, the repo/upload/artifact matches the state on the primary (i.e. "file not found"), so we will now mark it as synced.

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 Backend
  • Has been reviewed by Database
• Conform by the merge request performance guides
• Conform by the style guides
• Squashed related commits together
• End-to-end tests pass (package-qa manual pipeline job)

What are the relevant issue numbers?

Closes https://gitlab.com/gitlab-org/gitlab-ee/issues/5144 Closes #5312 (closed)