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helo, I just installed ubuntu mate 16.04 and installed CK2. The dir listed in the instructions for mods ~/.paradoxinteractive/Crusader Kings II/mod/ does not show up. Do I still need to create it from scratch?
I don't think this is the right forum for that question.
If I recall correctly, the mod folder is not created when you install/run CK2. Create a new folder, as you guessed, and put the mod in there. It should work fine (at least it does on Windows).
If you go into game and make a save file, I'd image that the CK2 directory would be created. Alternatively if you subscribe to a mod off of the steam workshop, the directory should be made.
A google search of your problem has other people creating .paradoxinteractive/Crusader Kings II/mod/, and that it works.