Another set of updates for RosettaCM.
- updated logic for fragment placement in stage 1
- updated domain parsing logic in realign_domains
- fixing bug in realign_domains where templates would accumulate drift over time (thanks Rocco!)
- better handing of realignment of ligand-containing poses
- removing more unused or redundant options
- small changes to smoothing kernel for fragment-derived constraints
- removing extraneous output accidently checked in in the previous commit
Hybridize and mr_protocols integration test changes expected.