Updates, still some type system problems
Merge branch 'master' of https://github.com/jgung/ClearClinical

Conflicts:
	ClearClinical/src/main/java/edu/colorado/clear/clinical/ner/pipeline/ApplicationPipeline.java
	ClearClinical/src/main/resources/semeval2015/TypeSystem.xml
Using YTEX WSD to select appropriate CUI
Cleanup, make sure training/test directories are in sync