Ignifex

It seems you are looking for glBindFragDataLocation, which tells glsl what output variable writes to which color target. By default, if only a single output is specified for the fragment shader, that variable is chosen as the output to the (first) bound color buffer.

 

Depth is a separate case, since only a single depth buffer can be bound at a time. No separate variable should be declared and it is not required to write to the depth manually. If you wish to do so anyway, you can use gl_FragDepth.

Just to point out a potential problem:

 

vec3 CalcPointLight(int _index, vec3 _normal) {
    vec3 LightDirection = worldPos0 - pointLights[_index].position;
    ...
}

 

It looks like your lightdirection is reversed with respect to your normal and eye vector. This could cause a lot te become black for the diffuse term and might mess up your specular computation as well (negative x in pow(x, y)), but it sounds like you solved that already.

 

What combination of lights have you used for testing? What happens when you use only a directional light?

I first noticed that your triangle is not interpolating between red, green and blue, but between cyan, magenta en yellow. So somewhere your colors are being "reversed".

Your problem is indeed in the code fragment you have shown below. The interpolation between corner points does not depend linearly on the distance, but the inverse of it. If the distance to your red point (d0) is very small, your "red weight" should be high.

You can have a look at Barycentric coordinates, which seem to most closely match what you are doing.

The second form, the "open" cylinder, is the common solution used in almost every model exporter available. The reason is exactly as you have mentioned.
Texture coordinates are not the only attribute that can differ per vertex on the model. Multiple normals are also commonly available, forcing even more splitting into multiple "single attribute" vertices.

To me at least, it is still not very clear what you are trying to achieve.
As for your direct question, you could have a look at the depth of the fragment you are drawing in your pixel shader, using eg. gl_FragCoord.z. You can compare this value to 0, which will usually be the depth value at the near-plane, possibly shade the fragment in a different way, and then modify the depth that is used to compare it using gl_FragDepth.