And in fact, I wonder if the idea of splitting everything into folders (EXCEPT NATIVE GAME CONTENT) isn't possibly the stupidest idea ever.
The *only* rational behind folderitis is being able to see select content easily. Why not sort by file type in Explorer or whatever file manager your operating system uses?
The first time I because anti-folderitis was when I realized that with replacement textures, modern Quakeworld engines -- which have a folder for every damn thing, you can't remember what the folder name for something is. Why should .lits have a folder? Even in multiplayer NetQuake, why should .locs have a folder.
Why do .mdl replacement textures in a modern QW or JoeQuake/Qrack go in textures\models ? .lit files are extra data for maps, they should go in the maps folder with the maps. .loc files are extra data for the maps, they should go with the maps.
Modern Quakeworld has too much history and content that depends on all of this to ever change, but I'm more point out that as any kind of standard it is wrong.
What made me think of this, is that I playing Travail with ZQuake to think about Quakeworld physics. And I saved my game.
I loaded up an NQ engine to play some Travail and tried to load that game. It said file not found, but I knew I saved it.
ZQuake saved the game into "travail/saves" folder

(FitzQuake also could load the save game, said something like "This is version 6 save game, not version 5". Honestly, I didn't have any idea save games have versions or a wrong format mechanism --- which is nice and offers hope. I might have been using DirectQ and not FitzQuake.)