Refactored StateStatementParser to share some of the methods with
CharacterStatementParser.resolve(). 
Fixed multiple to_id issues in Structure2Quality
Minor fix in PhraseMarker so  hyphened
phrases such as 'hyomandibula-opercle_joint' are marked properly
Changed the placeholder from "whole_organism" to "whole organism" in all
files. 
Merge branch 'dev' of
https://github.com/phenoscape/phenoscape-nlp.git into dev

Conflicts:
	phenoscapeII/src/outputter/CharacterHandler.java
	phenoscapeII/src/outputter/StateStatementParser.java
	phenoscapeII/src/outputter/Structure2Quality.java