restructured EntityParser and its calling classes so that 1.
EntityParser consumes the result of Structure2Quality strategy and
passes along possible conflicts (a <structure> may be an entity and a
quality) for the calling class to resolve, 2. also all entity parsing
requests will be processed by EntityParser.
Merge branch 'dev' of https://github.com/phenoscape/phenoscape-nlp.git
into dev

Conflicts:
	phenoscapeII/src/outputter/CharacterHandler.java
	phenoscapeII/src/outputter/Structure2Quality.java
	phenoscapeII/src/outputter/XML2EQ.java