Upgrade to ModeShape 4.0-alpha

- Port many of @cabeer's modeshape40 b/c kernel/kernel-impl reorg made rebasing modeshape40 branch very messy
- Update configs, fixing len/newlen bug in CacheLoaderChunkInputStream and updating JQL query in JQLConverterIT
- Update to Java EE 7.0, simplifying logging messages

Resolves: https://www.pivotaltracker.com/story/show/70387904