In answer to the first reply, yes, this is completely set apart from JK2 and JA. You will not need either game to run this program. The source will be in C++, and maybe a small scripting language built-in to do simple commands after compilation.
In regards to the Cease and Desist stuff, Outcast and Academy were built on the Quake engine. At the heart of this, I am just making an open source shooter that happens to also have sword support. If they tell me I can't do it, then I'll just say that and make the base game default to a Star Wars "Mod".
In fact, that is one feature I want in this: mod friendly. Maps, animations, models, textures, scripts, etc. should ALL be editable AFTER compiling the game. The launcher will then ask the player what "Mod" they wish to play. They select Star Wars, or Lord of the Rings, or some other mod and then the game starts.
The thing about this being open source is I want any coder who plays the game to say "geez, it would be cool if you could do __________ (<-- insert uber-cool game feature here)". After that, they code it and release it to the community and we could then incorporate it into the source.
So anyways, about the copyright stuff, it shouldn't be a problem.