I used to track WordPress updates, plugin updates and my own manual site changes using git. I wrote a whole post about it. Either fortunately or unfortunately WordPress launched their update framework which is so much easier than what I was doing. I’ve given up on my old technique and moved to using WordPress’ update mechanisms.
Of course what I really want is to be able to white a WordPress plugin that is notified any time an update occurs or a file update completes so that I can automatically track site changes in a SCM, but I don’t think that’s easy right now.