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So got a friend that only uses Linux for his gaming. He asked about this and I honestly could not find a discussion. Does the current modding system work okay in Linux?
BTLM and Modtek do have linux install instructions on their github pages so one would assume the mod manager works. If induvidual mods are writtten with the nessesary precautions to work cross platform is another matter but without having tested it yet I would anwer with a cautious: yes they should work.
What definitely does work is manually editing the .json files.
Haven't actually tried it at this point, since when the Linux version was finally released I was already addicted to the achievements you can get via GoG Galaxy... on Windows only.
In general though, if you have specific questions about getting stuff to work under Linux, I would most likely be willing to spend some time investigating.