A lot of changes in spirv-opt output.
Some new invalid SPIR-V was found but most of them were not significant
for SPIRV-Cross, so just marked them as invalid.
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.
Certain patterns with OpVectorShuffle (and probably others) will cascade
to so large, that they can cause OOM. After we have observed
force_recompile, don't spend unnecessary memory emitting code which will
never be used.
