[WIP] A collection of changes to the spec and pkg files to get working on garnet.erdc.hpc.mil

This is not ready to merge (still not working for hdf5 among other things), but I wanted to go ahead and start working towards a reliable stack for this CRAY XE6. I won't have  time to work in it again for several weeks.

Some of the original pkg descriptions do things before the prologue and so won't work on HPC environments that depend on first  loading modules. Relying on MPI_DIR set to the host_mpi install  directory, which contains nothing, is also a problem for some packages. In general I modified things to use the mpi compilers directly from $MPICC, etc., when MPI is needed. In several places I also modified the pkg files to extend  from base_package so the prologue would run. In others I explicitly specified 'after: prologue'.