in reply to
OT: Does anyone know of a version control system that doesn't use separate files or a repo?
Following up on moritz's comment: Mercurial at least (I've not used Git) adds a .hg folder to the folder containing the files/folders you are managing. It's not a lot of clutter and, as suggested, isn't going to take significant space on your drive.
If you are really worried by the clutter of one extra directory entry make the parent folder the root of the repo. Mercurial at least doesn't insert any additional "In your face" entries anywhere in the directory tree. Of course if you do go up a level then you may be able to place a whole bunch of files under revision control with no extra effort.
Perhaps however none of this helps in your situation, but as we don't know what that situation is it's kinda hard to address your real problem (if we haven't already).
True laziness is hard work