Barger oscillations

Here is my new pull request with a working version of the prob3 code incorporated into the template making chain. I have not combed through the code carefully and cleaned up things, so if you are looking for stylistic changes, you will find plenty of them! I had given the code a cursory look over in most places where I've made additions, but it is far from a finished product. The only reason I'm submitting a pull request now is because we want a version working so that others can have a look at it if needed. When I do have time after the posters/plots are made for neutrino 2014, I will go back through this and modify things so that they are more organized and sensibly written!