More configure cleanups.

-- Move Windows port checks to an earlier point, but after AC_PROG_CC and
   AC_PROG_EGREP are done, because it depends on both of them.  Also
   rename SYS to WIN32_SYS, because the former is way too generic and prone
   to clashes from elsewhere.
-- Removed some dead automake work-arounds that should no longer be necessary
   with the new automake 1.9 requirement
-- For Mac OS X universal builds, don't set CFLAGS/OBJCFLAGS/LDFLAGS so early
   with multiple -arch flags.  Set them at the end from UNIVERSAL_CFLAGS and
   UNIVERSAL_LDFLAGS.
-- Move set of INCLUDES down to final set of CFLAGS/OBJCFLAGS/LDFLAGS.

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