Fix a bug in CmakeHelper

When CMAKE_*_FLAGS are set in a package class, CmakeHelper.wrap_flags
should not override them.

Armadillo depends on Hdf5, not Mlpack.
Fix an obscure bug

When Hdf5 is built with MPI compiler wrappers, Mlpack which indirectly
depends on Hdf5 is needed to be built by using the same MPI compiler
wrappers.