Include johnswap.h in a bunch of files that lacked it.
BE fix in ZIP format broke strict aliasing rules.
Drop "missing library" warnings during configure now that they are listed
in the summary.
Autoconf: Comment out many tests that we do not use the results from. Just
cherry pick them back if/when we actually need them.
AC_JTR_FLAG_CHECK and AC_JTR_SET_NORMAL_INCLUDES broke MPI builds because
they were called too early: The MPI/CC test *must* preceed anything else
that uses/checks the compiler and/or the CC and CFLAGS variables.

This also has the effect we already got -O2 from AC_PROG_CC so we drop
the custom test for that.
Fix HDAA format for non-intel archs when OpenMP is in use.
Document Sparc build workarounds.