Add clean-up phase for ScheduleDiffFilesDeletion migration

What does this MR do?

Add clean-up phase to https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/20013 MR.

• Deletes temp index
• Process remaining jobs

What are the relevant issue numbers?

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/51469

Does this MR meet the acceptance criteria?

• Changelog entry added, if necessary
• Documentation created/updated
• Tests added for this feature/bug
• Conforms to the code review guidelines
• Conforms to the merge request performance guidelines
• Conforms to the style guides
• Conforms to the database guides