I've found a site that provides an overview of the OpenGL pipeline:
Now in the 3th phase (vertex processing) it says that after the transform feedback, there is the primitive clipping. If I am not mistaken, the primitive clipping must occur after that the vertices are multiplied by the projection matrix, otherwise it's impossible to determine if the primitives are inside or outside the view volume defined with glFrustum().
I know that in a typical GLSL shader you need to apply the modelview matrix to the vertices, so that you obtain a vertex in eye coordinates. So if I am not mistaken, at the end of the vertex shader you don't have vertices defined in clip coordinates yet. But this makes me think: where is the projection matrix applied? it seems like it's missing in this pipeline overview.