Working RESTful "hello world" program .

It hooks into the Query Engine API and reports on the rowkeys of tagsets and gives a protocol buffers representation of individual TagSets.
Update seqware-queryengine/src/main/resources/log4j.properties

Reset the logging level
pom.xml that allows both map/reduce client to work plus the jersey web service.
Merge branch 'feature/restSpec' of github.com:SeqWare/seqware into feature/restSpec
Removing javadoc from source.

It looks like the query engine spec was only checked into seqware.github.com which seems like a good idea.
Merge branch 'develop' into feature/restSpec
Merge branch 'develop' into feature/restSpec

Conflicts:
	seqware-queryengine/pom.xml
Minor fixes
Initial work on REST API with dummy pages for the various sections.
Merge branch 'develop' into feature/restSpec
Stubbed out some documentation before experimenting with swagger.
Merge branch 'develop' into feature/restSpec
Update swagger version
Merge branch 'develop' into feature/restSpec
Initially working swagger integration with minimal ReferenceSet output to JSON and PB
Working inheritance of Swagger annotations
Expanding REST specification to all sets and single element resources.

Most of the common methods on elements and sets have been stubbed out, but may be missing parameters and response headers.
Working embedded UI and some further additions to the specification.
Filling out some demo methods for Monday
Additional refinements to ignored json fields and other clean-up.