It works with Steam.Ahhh so it's a bit like the Nexus Mods Manager, but for FFVII? I assume it works on the steam version? I recall that being an issue back in the day. Now to see if it will play nice in Linux...
Really though, if you don't mind living with the OG 7 naming conventions for magic, mod the game with SYW on Windows and migrate that same install to whatever drive you're using with Linux, SYW doesn't require the mod loader active to start like 7th Heaven does.