Since Nexus Mod Manager for Linux fizzled out, I was excited to find a decent mod manager. It has built-in support for about 100 games, but adding other games seems pretty easy. I pasted in the Steam ID and path the the .exe of a proton game (MineMogul), and then everything just worked.
Do you have any experience using it with large modlists? Like a couple thousand mods at a time?
No, couple hundred at most.