Merge pull request #1355 from RosettaCommons/vmullig/update_rosettascripts_talaris2014
Switching some more defaults to talaris2014 from talaris2013.
Certain utility functions in RosettaScripts still default to talaris2013, and some default to score12. Updating to "commandline", so that they always stay in sync with whatever the default Rosetta behaviour is.