Track stage for varying sub-fields (#842)

Fixes #841

This reverts a small change made in #815 that seemed innocent at the time: we stopped tracking an explicit `Stage` to go with every `VarLayout` that is part of an entry-point varying parameter, and instead only associated the stage with the top-level parameter. That change ended up breaking the logic to emit the `flat` modifier automatically for integer type fragment-shader inputs for GLSL, but we didn't have a regression test to catch that case.

This change adds a regression test to cover this case, and adds the small number of lines that were removed from `parameter-binding.cpp`.
A few other test outputs had to be updated for the change (these are outputs that were changed in #815 for the same reason).

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