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