Renamed bioportal cache file, and also cache those that are unknown.

They can be unknown because the latest_submission returns an empty JSON
block.
Don't dump the bioportal cache

was only needed fro generation and future builds
Got building with maven and Java 7
Fixed warnings wrt generics and types
Fixes to remaining warning wrt generics
Improvements to detecting if an ontology is already loaded, and load if from the recorded source rather than ID