Move functionality to mdrunutility

Move functionality to mdrunutility

This lower-level module needs to acquire more content from mdrun as we
evolve a more levelised design. This change premptively resolves
several cycles that would be introduced by consolidating restarting
handling into mdrunutility/handlerestart.cpp.

Moved multi-sim related bools to its header, rather than commrec.h.
Several functions did not need to be inlined, as they were only
used during set up and tear down.

Made a few routines in even lower-level modules be passed the
boolean parameter computed from cr and ms, rather than being
passed it themselves.

Change-Id: I4a1721eaf7cbe08155110782a6680785091504db