Merge release-4-6 into release-5-0

Merge release-4-6 into release-5-0

Conflicts:
	src/gromacs/gmxana/gmx_energy.c
Eliminated time parameter (removed in release-5-0),
used gmx_ffclose (fixed in release-5-0).

	src/gromacs/mdlib/update.c
Eliminated fplog parameter (removed in release-5-0), otherwise added
new MTS-fixing functionality from release-4-6.

	src/programs/mdrun/md.c
Added new code path for MTS (from release-4-6), eliminated
wcycle and bInitStep parameters (from release-5-0).

Change-Id: I303bb649ed2373656aa4420d0afb27f738a9ea30