I ended up moving alot of the scripts into respective folders, just to help ease the clutter. As there are so many engine/base scripts and then the evaluation scripts, etc.
My biggest issue right now is sorting out the GUIXML tab, as it has tons of different ui's and I don't know that all of them are used in the demo/eval side of things. It also is the same on the repository, as the GUI and GUIXML folders have tons of the HJ textures, etc., but they're never referenced any more