The below walkthrough is for those who are running Fallout 4 via Steam Proton, and want to be able to manage mods via Vortex Mod Manager in Linux.
- If you have previously added mods through the Fallout game menu, I recommend removing them all since all mods will now be managed through Vortex. Mods => Load Order (T) => Options (V) => Delete All Mods. Also, consider taking a backup up your (vanilla) Fallout game directory.
# archive vanilla game (update archive path to suit your needs)
cd /mnt/gameData/archive
cp -a /mnt/gameData/Steam/steamapps/common/Fallout\ 4/. fallout-4