Ensure clean shutdown of repo on container shutdown

- Switch to ModeShapeEngine for deploy/undeploy/shutdown of repository
- Edit repo.xml files to reflect the new ModeShapeEngine and destroy hook on ModeShapeRepositoryFactoryBean
- Retool several ITs to create just a container context and get at beans via singleton pattern
- Some ITs were starting two repositories (in two different application contexts)
- Reintroduce a unit test and fix the auth webapp

Resolves: https://www.pivotaltracker.com/story/show/66454096