cd ~/.wine/drive_c/Program\ Files/Freelancer\ Mod\ Manager/mods
mkdir Discovery485
cd ./Discovery485
wget http://igiss.net/files/Discovery485.zip.flmod
unzip Discovery485.zip.flmod
Run FLMM and activate Discovery485.
I'm not sure why, but Discovery didn't automatically update, so I ran DSUpdate to install update 3.
Code:
cd ~/.wine/drive_c/Program\ Files/Microsoft\ Games/Freelancer/EXE/
wine DSUpdate.exe
After running into the sound loop bug, I tried using lame mp3 codec, but after that failed I copied C:\Windows\system32\l3codeca.acm from my windows install to ~/.wine/drive_c/windows/system32/winemp3.acm and specifying an override in winecfg. That's easy enough to do with the GUI.