I don't know if it's been brought up yet, but I've run into an issue with the files system. While working with mods for ZS samus, I accidentally hit "Remove resource" instead of "Remove mod files" for c05. now hitting "Reintroduce recourse" for the file does nothing, and once the mod it built and ran in smash, that alt is simply a copy of the default c00. It copies mods if they replace c00, and placing a mod in c05 anyway does nothing...
Edit: I should probably mention what I'm working with. I'm on sm4sh explorer 0.06.3, and I'm working with smash 1.1.5 (no I haven't updated yet. if it's just a bayo nerf it doesn't really matter to me...)