If your source list of files is read-only until a "commit" and only a single process is moving things around, you may be able to do this rather cheesily. For example, if you have an existing directory with files in it, and it isn't being modified, you can mirror it to a new directory, alter the files in the new directory, and then use a symbolic link (in Unix) to switch directories pretty close to instantaneously.

Other than that you or something your code invokes will have to keep a journal of every change made (as tye suggests) or if you feel lucky use something really cheesy like a copy-on-write filesystem.

bluto