I don't really understand ... when you run an update or a repair, why do you move files after it completed?
From my experience under Windows and Linux, you should not have to manually "finalize" the process. The update or repair process should have patched all files to a current state. But it may have left ZIP archives with difference information which it should have deleted instead after completing the patching process. If you try to unpack these and copy files out of them into your installation folders, it may be superfluous in the best case, but possibly destructive in the worst case.
I would be surprised if an update or repair under MacOS X would require manual afterwork. But I don't have a Mac, so, well, surprise me.