I think following line makes the problem:
transform.appendRotation(20, Vector3D.X_AXIS)
setting z = 0 I got half-cliped screen. I mean upper half screen is just solid gray background.
I think they are indeed far-clipped (if they have vertices with z>1 or z<-1 after the transform they won't be drawn). I copied the model-view-projection construct from the Utah Teapot demo at http://blog.kaourantin.net/?p=104 but you can probably merge the view (camera) and model matrices if you want.
Also, buffer 0 should be "float3" not "float4" (x, y, z), and I'm not sure what you're trying to do in the vertex shader. There are still some strange artifacts in my fork, I'm not sure what's causing them.
Your fork is exactly what I wanted! really thanks yonatan. I was trying to make a grid(done in this fork's original) and increase z of vertices according to their color strength.
In vertex program [add vt.y, vt.y, vt.z] part is.. just a wrong idea. I forgot that z value is set by z = (r + g + b) / 30 and tried to increase vertex's y coordinate by adding z coord to it, in vertex program.
I'm still messing around 3d projection math. to understand how it works I changed line 167, projection.perspectiveFieldOfViewRH, to projection.perspectiveFieldOfViewLH and some other changes. it looks good but I can't sure what I'm seeing is front face or back face. although culling is back I can see the mountain so maybe I have done correctly?