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

Some of these pkgs 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 is also a problem for some things. In general I modified things to use the mpi compilers directly when MPI is needed.
some Garnet fixes