Steam's Proton + Fallout 4 + F4SE + Mod Organizer 2

gistfile1.txt

A quick set of instructions to run F4 properly with F4SE and Mod Organizer 2.

Prerequisites:

* You are running Steam on Linux
* Fallout 4 is present on your account
* protontricks installed in your system (https://github.com/Matoking/protontricks)
* Distro is not important

Installation:

* Install game as usual (i.e., open Steam, select the game in the library, click "Install")
* Launch it once without any tweaks
* Download Mod Organizer 2 from https://www.nexusmods.com/skyrimspecialedition/mods/6194?tab=files
* Open a console, change directory to one you've downloaded MO2 installer to
* Launch MO2 installation via protontricks-launch: protontricks-launch --appid 377160 ModOrganizerSetup.exe

NOTE: you might need to change the file name of the actual installer here to the one you might have)

* During the installation, choose for MO2 to be installed within the directory of the game in a subfolder (i.e., [...]/steamapps/common/Fallout 4/MO2/)
* Finish the installation
* Download F4SE from https://f4se.silverlock.org and install it as usual (i.e., copy its files in the appropriate fashion to [...]/steamapps/common/Fallout 4/ directory)

NOTE: now would be the time to install native code mods requiring F4SE, if you'd like to use any

* Now select Fallout 4 in your Steam library, right-click it, and select "Preferences"
* On "General" tab adjust your launch command so it would look something like that: bash -c 'exec "${@/Fallout4Launcher.exe/'MO2/ModOrganizer.exe'}"' -- %command%

Now you can launch the game as usual via button in Steam library, and MO2 will launch instead of game's launcher. Now you may install, uninstall or otherwise manage any mods. 

To run the game, select the preferred launch option (Launcher, F4SE, etc.) and click "Run".

Now you can launch the game as usual via button in Steam library, and MO2 will launch normally. Now you can install the mods that you need.