Updated Gitaly and Praefect config for new 16.0 format

What does this MR do?

The MR adds back Update Gitaly and Praefect config for new 16.0 ... (!986 - merged) which was reverted due to a bug 500 errors 'GetRepoPath: not a git repository' ... (gitaly#5039 - closed). As investigation showed, if a path in git_data_dirs is configured, /repositories is added automatically. This doesn't happen when gitaly['storage'] was used.

The MR adds additional commit to add /repositories per gitaly#5039 (comment 1344005023) - 329204cd since GET used git_data_dirs and didn't use gitaly['storage'].

Related issues

gitaly#5039 (closed), #651 (closed)

Author's checklist

When ready for review, the Author applies the workflowready for review label and mention @gl-quality/get-maintainers:

• Merge request:
  • Corresponding Issue raised and reviewed by the GET maintainers team.
  • Merge Request Title and Description are up-to-date, accurate, and descriptive
  • MR targeting the appropriate branch
  • MR has a green pipeline
  • MR has no new security alerts in the widget from the Secret Detection and IaC Scan (SAST) jobs.
• Code:
  • Check the area changed works as expected. Consider testing it in different environment sizes (1k,3k,10k,etc.).
  • Documentation created/updated in the same MR.
  • If this MR adds an optional configuration - check that all permutations continue to work.