Some honest feedback, this will really help if you can make this change. When you say "body", this should be your naked character (we call this character base in pixel art). Everything should be its own piece/folder. You're doing this 90% already, with accessories, hair, etc. Why? Game engines will allow users to "build" their own characters, by combining naked body, clothing, hats, etc.
So I'd recommend splitting out the "bodies" because currently, they're not bodies. they're body+clothing that is inseparable.