The only solution I'd believe to work here would be to force the launcher to update those files every time you start the game; and then make server unable to join without people using Launcher.
Colored arrows/bolts/throwing things/ weapons etc and invisible walls/bushes are huge advantages and definitely 100% cheating. If I could 100% prove anyone to be cheating I would ban them but then I would never know when I could trust them to not be cheating or 100% certain they are cheating so pretty simply put admins can't do much.
It is 100% cheating, and your solution was exactly what I was thinking. It would be very easy to verify (or change) files that have been altered before joining the game, and if your files don't match up with the default textures, you can't join.
that would overwrite finalboss' heirloom pack, calradia in darkness and similar mods that improve the gaming experience
need to add exceptions, and then people would find ways to work around it
best to downvote pandor into oblivion
Like Heskey said, you could white list certain files. Or my preference would be "tough fucking shit". Having "pretty" textures from final boss, or letting people cheat in the game...hmm which is more important here. Should be pretty obvious that if we can stop cheating, but it means no more final boss textures, we stop the cheaters.