Handle optional dependency MPI by directly passing HAVE_MPI flag

Summary

This MR changes the way optional dependencies are enabled in cmake, following the MR !1294 (merged). Essentially the add_dune_xy_flags function and the dune_register_package_flags now sets HAVE_XY directly instead of writing a config.h entry and setting ENABLE_XY afterwards.

In this MR the package flags for MPI are updated.