House-keeping for MTTK

Leapfrog + MTTK silently produced a .tpr that is probably broken;
certainly the documentation only states support for Velocity-verlet
integrators.

Added note about deprecation and planned removal of MTTK + constraints.

Refs #1292

Change-Id: Iec2cf0dd866242735ce04a954e585b2461f6e701
Fixed bug in parallel v/f constraining

Constraining v or f with 3 or more decomposition domains in one
or more dimensions could lead to modification of communicated
v and f components by the box size for inter charge-group constraints.
Fixes #1462

Change-Id: Idece9d2d0d8f48e65a654d5c2892fbe1ff836ba0
Merge branch release-4-6

Change-Id: Ie4431fb0002cd36799c8e664dcf4e096e66bc0ea
Keep CMake quiet about non-detection of optional stuff

Repeated calls to cmake would otherwise warn every time that these
optional things were not detected. That lack is only rarely a problem
that needs solving, so they should not be emitting status messages all
the time.

Change-Id: Iad6f0bdf72ba7848bcc819db6937b70b37900148