Reorganized domdec initialization

Reorganized domdec initialization

The number of external domain decomposition initialization calls
has been reduced from 5 to 2. The zone setup has been moved up,
in preparation for vacuum support for the Verlet scheme.
The number of PME ranks now get passed to init_domain_decomposition
as an argument instead of setting cr->npmenodes in mdrun.cpp.
Removed the (buggy) option for sorting cgs less frequently.
Also added const qualifiers for parameters in all domdec functions.

Change-Id: Icf320ff3b9c86b782ddbde5ed6dd5013dff8c2a8