Our shader/particle/trail files are quite messy, due to both the constant asset updates and the mixture of leftovers from Tremulous. So, what I've wanted to do, in order to make it easier on ourselves and our future efforts, is to make a coherent set of unified script files. For instance, a weapons.shader would have the shader entries for all of our weapons in a single place, with all of the redundancies removed. I also want to maintain it over subsequent releases, appending new material to the same files, so that by the time we reach beta we don't have to do this all over again.
What do you feel are some good groupings? The weapons.shader example is what I'm thinking of, and obviously an aliens.shader for all of the individual aliens in one file. I could be wrong, so tell me if you have a better organization idea.
Also, should I be removing all of the references to old Tremulous assets that we don't use, or are only used by players with the high poly option turned off?