Working implementation of settable experiment_spot_design and experiment_library_design.

Supporting work includes web resources for experiment_library_design, experiment_spot_design_read_spec, and experiment_spot_design (for error checking). This includes tests for those web resources and tests for modifications to the MetadataPlugin in order to access the two new fields. Modifications to Jaxb (lists of convertable classes), context, and existing experiment web resources were also made.
SEQWARE 1579, 1724 Support creation of root samples while adding a constraint to avoid duplicate sample_hierarchy entries

Users will need to run the update script while the existing MetadataPlugin should now function correctly.
Added more explanation and a demonstrating test
Make test even more explicit
SEQWARE-1682 - Test retrieval of annotations from the new study report
Ensure that we close the Hibernate session properly
Hook seqware into Maven build process and demonstrate a simple test using Maven properties to locate built script
Update ubuntu_12.04_gridengine_script.sh

I think edit commands are needed since many of these are already setup by the apt-get install.  Testing now.
Refactoring strings into enums.
SEQWARE-1710 - Hook the extended integration tests into the new CLI
Appease JAXB by changing Foo.Status to FooStatus.
Move SequencerRun.Status to SequencerRunStatus
Ensure script permissions and fix up inherited test
I think I fixed the problem with skip-it not working, added skip-launch so you can debug configs, and modified the SGE setup process.  Need to test the latter.
Tell hibernate to convert enums to strings.
Fix a couple of laggard refactorings
Account for default behaviour of new command line

Need to direct output to files and relax the output checks
Move hibernate enum annotations from field to getter.
Fix up format of new CLI output to match old filters
Use hbm mapping instead of annotations for enums.