Yeah the rest are from the Steam WorkshopI'm not familiar with Linux at all, but if that's where you have your gfx folder for example, then that's the right place to have created your mod folder. According to the wiki, this is the path for Linux: ~/.paradoxinteractive/Crusader Kings II
Also, I find it curious you have a bunch mods already. I'm assuming you've been using the Workshop up until now. Unless I'm misrembering you should have already have a mod folder.