Resync with Yank/openmmtools

[mrshirts]

Currently uses a version of Yank(version 0.21.2) that requires changing one line of the Yank (version 0.21.2) code by hand in order for replica exchange simulations to run properly (line 1600 of yank/multistate/multistatereporter.py must be changed to: "storage.variables['positions'][write_iteration, replica_index, :, :] = x[:][:]").

The best fix is to update to a newer version of Yank, though this will require some update to the code, as it currently has moved the multistatereporter.py to OpenMM tools.