Merge release-5-0 into master

Merge release-5-0 into master

Conflicts:
	docs/install-guide/install-guide.md
Applied release-5-0 changes to docs/install-guide/index.rst

	docs/manual/install.tex
Applied release-5-0 changes to docs/user-guide/environment-variables.rst

	src/gromacs/commandline/cmdlineprogramcontext.cpp
Applied comment from release-5-0

	src/gromacs/gmxana/gmx_hbond.c
Removed smooth_tail as in release-5-0

	src/gromacs/gmxlib/gmx_detect_hardware.cpp
Removed GMX_MAX_THREADS implementation as in release-5-0
(adjacent changes)

	src/gromacs/utility/init.cpp
Combined changes to include statements

	src/gromacs/utility/path.cpp
Combined changes to include statements

	src/programs/mdrun/mdrun.cpp
Added new please_cite calls from release-5-0 to new call site
in runner.cpp

Change-Id: I5b75b12bb8a49a606b086184017b754477d65068