Major refactoring to handle new-style annotations
Merge branch 'master' into new-annotation-structure
Cleanup and Badgerfish compliance
More migration to new annotation structure
Recognizing new annotation structures in old code
New annotation integrity, fixes for mapping hints
Merge remote-tracking branch 'origin' into new-annotation-structure
Fixes for supporting-files and mapping-hints

Ongoing migration to new annotation structure.
Badgerfish cleanup of OTU-mapping search context
Misc fixes for new supporting-files annotation

Includes Badgerfish rules throughout, and initial client-side testing.
Merge pull request #169 from OpenTreeOfLife/new-annotation-structure

Refactoring for new annotation structure