Multiple Pass Shaders
I know this is more complex but for things like hair, it's pretty important.
http://forum.unity3d.com/threads/167762-Hair-shader-with-Kajiya-Kay-specularity-and-proper-sorting
Our hair shader does an alpha clip on the skull cap then an alpha blend on the outer layers.
Solution
Yes, this is rather complex! Currently passes are auto-generated for things like multiple lights, distortion etc. I'm considering making a special multi-pass mode later, where you have full control, but less automatic things helping you.
I reckon that would be totally fine, reality is once you want/have to go multi pass you probably do want that kind of control. Interestingly I can't seem to find a way to pass the results of 1st pass to a 2nd pass in a surface shader (the actual texture pixels) be cool if that were possible.
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Yes, this is rather complex! Currently passes are auto-generated for things like multiple lights, distortion etc. I'm considering making a special multi-pass mode later, where you have full control, but less automatic things helping you.