If you're developing really specific functions for yourself, it's probably not a good idea to add this to FreeMat's source code. Most of us have quite a few of our own m-files that allow us to do different things we're interested in, but the things that get committed to FreeMat's code structure tend to be specific features users have requested that seem like they would be useful for other users.
Are you looking just to modify the source code yourself for your own purposes, or are you looking to add your specific m-files to the overall functionality of FreeMat?
TJ