Merge pull request #3427 from RosettaCommons/roccomoretti/parse_resnum_RID
Use ResidueIndexDescriptions to remove Pose useage in parse_my_tags()
This updates a number of diverse classes which did (Pose-dependent) residue number parsing in parse_my_tag(). Now they create and store ResidueIndexDescriptions instead, deferring the pose-dependent parsing until apply time.
This updates ResidueIndexDescription for output and serialization, and adds a few new ResidueIndexDescriptor subclasses, such as "end of chain" and "last residue in pose". It also makes a pose-free version of parse_resnum() which returns a ResidueIndexDescription.
The bulk is the conversion of various Movers & Filters to use ResidueIndexDescriptions versus in-parse_my_tag pose use. As an added benefit, certain classes which used to take only Pose-numbered parameters can now also take PDB numbered parameters.
I shouldn't have changed any existing functionality.