GitLab

* Replace SimTK-containing file headers

* Update file headers for new Tinker reader files added

* Created OrientationRestraintForce

* Python API

* Documentation

* Serialization

* GPU implementation of OrientationRestraintForce

* Bug fix

* Remove unused code

Refactored ForceImpl, lots of KernelImpl subclasses, and other related classes to avoid redundant calculations when requesting a State with both forces and energies

Free energy plugin added
Plugin will not run w/ Obc or GB/VI forces unless line 2004 of gpu.cpp (gpu->sim.totalNonbondOutputBuffers  = 2*gpu->sim.nonbondOutputBuffers;) is commented in -- working on removing this constraint
Also unit tests for GB/VI currently fail 

Changed how kernels get initialized.  StandardMMForceField now has you set the 1-4 interactions explicitly.  CMMotionRemover allows the removal frequency to be set.

Modified the initialization order of ForceImpls to prevent them from trying to initialize themselves before the Platform had been chosen

Created a test case for StandardMMForceFieldImpl's findExclusions() method.  Fixed some bugs that it found.  Created a CMake script and configured it for building and running test cases.