Working on embedded jetty running
Trying to get this to work in either jetty or tomcat. No luck yet.
Revert "Trying to get this to work in either jetty or tomcat. No luck yet."

This reverts commit 8ecb2d6d181d65f4c2151a2ce7af404c667e94a1.
This gets mvn tomcat6:run working with the base web service.

Next to automatically publish the base docs
Redirect web ui
Update swagger docs
Update swagger ui based on https://github.com/wordnik/swagger-ui
Update web service API for swagger 1.3.0 compatibility
Update README.md with new instructions
Merge branch 'develop' into feature/SEQWARE-1739_simple_webapp_for_qe
Merge branch 'feature/SEQWARE-1739_simple_webapp_for_qe' of github.com:SeqWare/seqware into feature/SEQWARE-1739_simple_webapp_for_qe
Merge branch 'feature/SEQWARE-1739_simple_webapp_for_qe' into feature/qe_disable_optimization

Conflicts:
	pom.xml
	seqware-distribution/pom.xml
Refactor query engine web service into separate module so that we can run command-line tools AND web service successfully via mvn tomcat6:run