Geo: Ensure that file and repository deletions are communicated to the secondary

We've seen a number of issues where LFS objects and repositories have been deleted from the primary, but their entries in the tracking database have been left in place. This causes odd results such as 14/13 repositories synced, or 10000/500 LFS objects synced (both seen in reality).

We should verify that:

• The deletions for every type of file and repository are communicated to the secondary via the event log
• The secondary removes the file / repository from disc if appropriate (ignoring object storage-backed ones)
• The tracking database entry is removed

Related MRs:

• Repositories - https://gitlab.com/gitlab-org/gitlab-ee/merge_requests/3440
• LFS Objects - https://gitlab.com/gitlab-org/gitlab-ee/merge_requests/3481
• Attachments see https://gitlab.com/gitlab-org/gitlab-ee/issues/3962#note_47744528