packages.mk: disable parallel build for HDF5, add ninja

By default, HDF5 is now configured without the --enable-parallel flag,
as it requires MPI to be installed which is not required by HALMD. It
can be enabled by "ENABLE_PARALLEL_HDF5=1", though.

Further, add ninja - an alternative to GNU make to the packages. In
order to generate ninja build files with cmake, use
  cmake -GNinja <source-dir>
doc/pdf: fix build for ninja

Split the LaTeX and PDF generation into separate commands and explicitly
call "make" instead of ${CMAKE_MAKE_PROGRAM} because sphinx will always
generate a Makefile and the make program can be different.