Some users have recently had their accounts hijacked. It seems that the now defunct EVGA forums might have compromised your password there and seems many are using the same PW here. We would suggest you UPDATE YOUR PASSWORD and TURN ON 2FA for your account here to further secure it. None of the compromised accounts had 2FA turned on.
Once you have enabled 2FA, your account will be updated soon to show a badge, letting other members know that you use 2FA to protect your account. This should be beneficial for everyone that uses FSFT.
I don't believe you can put those setting in the client.cfg file. I think they HAVE to be done on the command line, I.E.
FAH4Console.exe -advmethods -forceSSE
cd /your/folding/directory
./FAH4Console-Linux.exe -advmethods -forcesse
If you want it to run in the background, add " > /dev/null &" (without the quotes) to the end of the launch command.
If you have permission errors and its a first time setup, odds are you need to make it executable-
chmod +x /path/to/FAH4Console-Linux.exe
You can also create a shortcut that has the flags just as you would in windows, but that sort of requires a gui and the method will depend on what gui you're using.