I've decided to make a brand new Nexuiz map. I have run into a few issues I can't for the life of me resolve, and seem like engine issues to be honest.

I am using an SVN client, SVN q3map2, and GtkRadiant 1.5.0 SVN(right before the SVN went to ZeroRadiant).

1. Clipping results in disappearing any surface it touches. This is annoying me because my stairs have diagonal edges, which look nice, but slow down the player when moving up them. I want to use clip to fix this problem but it is just making the steps disappear.
2. Water, although with "surfaceparm water" set, is solid(and I even tried using surfaceparm nonsolid, to no avail). I am using the water shader on top, and the nodraw water shader on all other sides.

I'll update with more issues I have found.

Consider using NetRadiant which is way better than 1.5.0 or zero.

http://forums.alientrap.local/viewtopic.php?t=3687

Your issue is clearly a wrong shaderlist.txt. Did you make that file? Do you perhaps have PK3s installed that contain a bad shaderlist?

Take out ALL your pk3s out of ~/.nexuiz/data and try again.

shaderlist.txt contains common, as well as my shader script. Keep in mind, my water is correctly rendering reflections(with dp_water), so the shader is in fact working.

EDIT: I've fixed it by symlinking shaderlist.txt to my ~/.nexuiz/data/scripts/ directory.