It was long ago when I installed the Half Life Quakux mod but I do remember some things I did to make it work (with help from fuzzi23). Here are the files I had in my Quakux folder:
Inside the
Quakux folder, you should have the
ID1 folder, the
valve folder, the
Quakux file, and
HalfLife.dge.
Inside the ID1 folder you should have these files: config.cfg, Pak0.pak, PAK1.PAK.
Inside the valve folder you should have these files: (gfx folder, MAPS folder, MODELS folder, PROGS folder, SOUND folder, SPRITES folder, autoexec.cfg, CONFIG.CFG, dingoo.cfg, gfx.wad, progs.dat, quake.rc)
Make sure you
do not have the Pak0.pak, or PAK1.PAK files in the valve folder or the game will not launch.
Hope this helps!