As a caveat, file alterations get sticky when you move between versions. Part of the problem lies with PCGen itself; there really is no version control worth the name, so that as more files are piled on, they sometimes supercede, sometimes complement, and sometimes simply co-exist with, files which do the same thing. There is usually no attempt made to prioritise or even weight different files from different sources, so it can be tough to find the "correct right file" that **really** adds the capabilities you want, or eliminates those you don't.
Obviously, as big a pain in the ass as it is, always make a "Masters" folder/directory and stick an unaltered copy of the original file in it *before* you start making changes.
Keep in mind that if you add or alter source loads, you may get unexpected results, because of the poor control of what lives where. I've not used plain 3.5 in years---I use Pathfinder, which is a 3.5 derivative---so I'm not sure where you'll find you're file exactly, but they are **always** in the "/data" directory of the branch you're using (3.5, Pathfinder, 4,5, 600, etc...).
I disagree about Homebrew support, as I consider it weak and unreliable. Just be sure you keep a faithful copy of your customised files **outside** of the root tree of PCGen, that way you can re-integrate the changes whenever (a) a new release of your version comes out; or (b) some one decides they don't understand what went on in PCGen Version X and decides to perform a "do-over" which screws up all existing files (aka "new version" release).
Remember that a core rules file may be superceded by a supplementary file, so re-post if you don't find the file you're looking for and I'll take a look (I do a lot of languages, races, magic item stuff myself).