the first thing I've noticed is that, by default, prboom-game-server links against the SDL libraries. This might simply be a result of the way it is built at present, rather than a requirement, however.
I can confirm this. The prboom-game-server binary is linked against libSDL_net-1.2, which in turn is linked against libSDL-1.2. The latter will pull in libX11 and the sound output libraries, anyway.
So, the only direct dependencies that would be saved by a dedicated prboom-server package would be "libgl1-mesa-glx | libgl1, libglu1-mesa | libglu1, libpng12-0, libsdl-mixer1.2". I am not sure if this is a real win.
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