Merge pull request #170 from RosettaCommons/daslab
All changes related to constraint_set use, mainly to get them working for stepwise applications.
All changes are 'cosmetic', as noted in comments to pull request, with removal of warning
"core.scoring.ConstraintSet: ERROR: HUH?!? weird stuff is going on. ConstraintSet is hearing disconnection voices that it shouldn't"
Also changed back option constraints::exit_on_bad_read to true rather than false -- this would have caught several of my jobs that were silently reading through constraints in the wrong format.
In cases where a pose is deleted or copied, and the constraint set then is checked -- there's actually a flag conformation_pt_.expired() that says the constraint set is out of date -- now check that before printing warning.
See notes on pull request for changes to a few tests that do not run or appear unusually sensitive to small changes.