Merge release-4-6 into master

Merge release-4-6 into master

Conflicts:
	CMakeLists.txt (just version)
	src/gmxlib/confio.c (just whitspace)

Moved gmx_thread_affinity.[ch]. Removed from it the visibility.

Doesn't include copyright and unrustify commits

Made by:
git merge -s ours 95761d63fb705b4334acbe2ce6ae2f384b4bcadb
git merge 66ff3d6e8bf65cce7b3008e65719e333da5e83e3
git merge -s ours 3339ffd6be2736541b928446de39ce51293449c6
git merge origin/release-4-6
tree=$(git log -1 HEAD --pretty=%T)
git reset --hard $(git cat-file commit HEAD | sed '1,/^$/d' | \
    git commit-tree $tree -p 03d5ecd -p bb6ea98)

Change-Id: Ibce56da97e270cf3f399cfdc89684917afc96a33