Removed dependency on commrec of mdrun setup

Removed dependency on commrec of mdrun setup

Changes no functionality.

Setup is now parameterized directly on MPI_COMM_WORLD, which we will
want later for letting library-based callers pass in an
MPI_Communicator. This permits commrec to be initialized later, once
the threads have been spawned for the thread-MPI ranks.

The initialization of multi-simulations moves from LegacyMdrunOptions
to SimulationContext, which is more appropriate for
ensemble-parallelism established directly by the user.

Before the decision about the duty of a rank, there is no difference
between MASTER(cr) and SIMMASTER(cr), so several calls to macros
taking a t_commrec pointer are replaced by booleans. Introduced
findIsSimulationMasterRank to compute that value. This eliminates
early use of t_commrec that has necessitated other hacks and
workarounds.

Removed redundant check for replica exchange when the number of multi
simulations is less than two, because gmx_multisim_t constructor
already prohibits that.

Resolves several TODO items and improves modularity, too.

Refs #2587, #2605, #3081

Change-Id: I48bd3b713bc181b5c1e4cbcd648706a9f00eab96