Merge pull request #3223 from RosettaCommons/rpavlovicz/water_ddg
This commit is a major refactor of PR #2825, removing a lot of code from core into protocols.
* all the point-water code, including generation and packing, now lives in WaterBoxMover. This mover is parsable with only 3 options:
<WaterBoxMover mode="replace"/>
Mode is one of (remove, append, replace), and the mover carries out all steps of the protocol.
* water overlap code logic is rewritten to be faster
* bunch of options removed (where default values were generally reasonable); option system calls centralized to one function
There are many expected integration test failures:
* 20 result from changing RestrictToInterface (removing dependency on interaction graph)
* 49 result from showing EnergyMethodOptions on stdout (several defaults changed)