Implementation of test.

Follow up with a few tests to lock-down behaviour.
Revert bizarro side-effect of NetBeans refactoring
Associated tests for new stdout and stderr output for GCR
Add exit code to standard reporting
Fix up context file path for mvn tomcat6:run
Merge pull request #56 from SeqWare/feature/SEQWARE-1242_integration_tests

Feature/seqware 1242 integration tests
Merge pull request #57 from SeqWare/feature/SEQWARE-1614_arbitrary_host

Feature/seqware 1614 arbitrary host
Merge pull request #58 from SeqWare/feature/SEQWARE-1668_gcr_output

Feature/seqware 1668 gcr output
Merge branch 'develop' into feature/SEQWARE_1683_default_workflow_engine