The .baf files are the model files. They are basically compiled versions of the original .3do and .key files from the original Jedi Knight file format, in addition to the .mat texture files, all bundled into one. They also contain several flags we use for damage tags etc.
We used the existing JK file formats because it saved us quite a bit of time. There was a little tweaking involved, but all in all, the JK stuff worked just fine. We just spent more time getting the lighting correct for TPM.
Now, if you REALLY want to start taking chances, if you copy a .baf to one of the player characters (like: sithjedi.baf renamed to obiwan.baf) and then move the copy into your TPM root directory, then it will boot up the game with that model as the playable character. WARNING: in most cases, all you can do is walk around. If you attack, or shoot, or do anything, or even GET shot, the game will probably crash, because most of the animations will be invalid. Just something for the TRULY hardcore-TPM fanatics.
Here are the names of the playable characters:
Oh, and be sure to make backup copies of everything. Just delete/move the modified .baf file out of the TPM root directory to restore the original characters.
Yes, this is how I would also instruct you how to play the Mace Windu .baf file should I get permission to distribute it.