Wrong. Linux is still a unix system. And unices aren't graphical. Well, it's actually not a unix, but it's a unixish system. But Mupen also runs on *BSD - and that are real Unices

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Noone needs more then a terminal, screen, a XServer and evilwm as Window Manager, that should be enough for everyone. On Windows, it's different. There everything really needs a nice GUI.
I would support the idea to have a command line version of Mupen64.
Eg. ./mupen64 ../roms/Mario_Kart_64.v64.gz
That would be much more user friendly since you don't need to click around in the GUI.
Even for KDE Users (Sigh! Who needs KDE?) this could be an improvement: They could just add the mupen64 binary for *.v64 and *.z64! And then with one click launch the game.
So this could make terminal-lovers like me and KDE users happy.
But that doesn't meen that the GUI needs to be removed, oh no! I just thought about having a way to compile it without the GUI and a way to compile it with GTK+ or Win32 GUI. That would be nice as an option for the ./configure Script, for example --disable-gui, --enable-gui=gtk, --enable-gui=win32 and so on.