Remove charge groups from domdec and localtop

Remove charge groups from domdec and localtop

Code explicitly handling charge groups has been removed in the domdec
module. Removed the charge groups from gmx_localtop_t.
Changed cginfo in forcerec to std::vector, which propagates into
the nbnxm module.
Parts of the TPI code are now commented out until reimplemented.

Change-Id: I9d3bffe26e34ebbb8e31ef97a9a7f1e0bea92306
Todo: Change naming from charge group to atom.
Todo: Remove duplicate counters for atoms and charge groups.