Encapsulate gmx_wallclock_accounting_t into new timing module

Encapsulate gmx_wallclock_accounting_t into new timing module

Started a timing module where things like gmx_wallcycle.c and
gmx_cyclecounter.c will eventually also live.

Renamed s/runtime/wallclock_accounting/ to avoid ambiguity with
"compile time," "simulation time," etc.

This patch preserves the release-4-6 behaviour of the reported times
with all supported combinations of MPI, thread-MPI, GPUs, OpenMP.  I
think the old behaviour of -ntomp_pme != -ntomp was buggy with respect
to timing, and this patch fixes that.

Change-Id: I22cba17cdf866e17d9d0732de204b85b0ab31994