The code didn't deal with explicit function indexes properly.
It also handed out the indexes at link time, when we really
need them in the lowering pass to create the correct if ladder.

So this patch moves assigning the non-explicit indexes earlier,
fixes the lowering pass and the lookups to get the correct values.

This fixes a few of:
GL45-CTS.explicit_uniform_location.subroutine-index-*

Signed-off-by: Dave Airlie <airlied@redhat.com>