gallium: move the test for bypass_vs into the vs_XXX_run() functions

gallium: move the test for bypass_vs into the vs_XXX_run() functions

Also:
1. Added an identity_viewport flag to skip viewport transformation when it
has no effect.  Might also add an explicit bypass_viewport flag someday.
2. Separate the code for computing clip codes and doing the viewport transform.
Predicate them separately.
Note: even if bypass_vs is set, we still look at the shader to determine the
number of inputs and outputs.