Im talking about ~/.fs2_open/fs2_open.ini. can I see an example that includes things like mod folders and switches?
Mod folders and switches are not stored there. fs2_open.ini stores things the the resolution, bit depth, etc. (the stuff that is stored in the registry on windows) which are set by a launcher. Run a launcher once, and it will setup the file and then you won't have to bother with it any more, especially becuase the resolution can be set by -res.
Mod folders and the other commandline switches are stored in the <game data folder>/data/cmdline_fso.cfg as a single line. Though because you are on linux you can either just put the switches into a shell script and pass them to FSO directly on the proper command line, or you can put the cmdline_fso.cfg file in ~/.fs2_open/data/cmdline_fso.cfg.
