ok...for each mod release some of us devs go trough mod files and delete redundant ones...but that process is long and brings some risk of deleting file that is actually in use...
So i am sure we will do the same for new release...in that case best solution is to uninstall the game, delete any folders left after deinstallation, and make completely fresh installation and mod activation. Then in your game folder you will have only newest of all files and game performance may be slightly better. It also eliminates possibility of strange bugs.