I`m just don't use mod folder and work straight with game files. Partly bc i have too many changes in different places in files. Trying to separate mod from core gonna be my headache for weeks if not more, So just replace game files, it can solve you problem.
UPD. Also its easier for merging old files with new game version, u can see by yourself what changes new and how they work now. Save a lot of time, really.