Eliminate main.h

Eliminate main.h

This generic file had generic content and will create cyclic
dependencies if not broken up into logical units.

Moved replica exchange code to be alongside the multisim code that it
needs. Moved multi-sim communication routines to be where other
low-level and multi-sim communication routines are found. Added simple
Doxygen, while leaving a suppression and TODO for the main
replica-exchange routines documentation, which is not in scope for
this change. Converted a define to a constexpr and made the include
guards match GROMACS style.

Change-Id: I123231d56bfa9a699ddbd32fec0b055cf14d93e3