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If you want to add something like an alpha override instead of just putting the alpha in the diffuse alpha layer like you should, then you can pick a texture # between 6 and 10 and add that texture in there. Then write a super simple shader mod to just get your alpha from that B&W map instead of the diffuse.
Include Files
Compared to usual GLSL shaders you can use #include to have include files. It can help organise your code and any similar code can be put into include files instead of the base shader file. The main thing is when #include is found it will copy the entire file contents to where it is defined.
One major thing that won't work with them is #if blocks - #include files are always included - so make sure you instead #if block all the include if it is specific to a particular platform/uniform/define.
How Does NWN Load a Shader
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