[fly_zo]

Game loads any file just once .... first file that it finds !!!

... modded game checks and loads files by this order:

1 from Mods folder alphabetically

a) first get loaded hashed files present in any mod ( those which looks like ABX435XX512XX )

MODS\ "any mod folder" \ ABX435XX512XX

b) rest of files present in subfolders in any installed mod

MODS\ "any mod folder" \ "game structure subfolder"\.....

2 from Files folder

only files which hasn't found/loaded from Mods folder

3 from game root

first from SFS files and then from folders in main game directory

again, only files which hasn't loaded from Mods or Files !

So basically you can get rid of any "double" folders/ files without problem ( respecting upper explained order) and game will work just fine .
Removing any default file/folder from game root directory is risky business cos you must be absolutely sure that you have all needed files present in Mods or Files folder before such action ... and since game doesn't load double files they have no influence in game performance whatsoever , all that you can gain from such action is some free disk space , nothing more .

Hope this explains it ...

Z