You need a mask image. I actually have the one Cardigan made. IIRC, PJW had the idea and Cardigan made it.
The mask rolls around behind the sky and shows up through the cloud layers.
One of my first ever maps, Tyger Tyger or something stupid I called it, uses the shader and mask layer. Look for it on lvlworld. It's an old fashioned sky shader though, non of the q3map2 keywords.