Implement this by flattening outputs and unflattening inputs explicitly.
This allows us to pass down a single struct instead of dealing with the
insanity that would be passing down each flattened member separately.
Remove stage_uniforms_var_id.
Seems to be dead code. Naked uniforms do not exist in SPIR-V for Vulkan,
which this seems to have been intended for. It was also unused elsewhere.
