[ADAM-309] Update to bdg-formats 0.2.0

- Some of the files have been renamed as part of the renames in
  bdg-formats
- I cleaned up some of the references in the files, as well as some of
  the IntelliJ complaints in the files
- Adding ClasspathFileLocator to allow testing local files
Merge pull request #342 from genomebridge/bdg-formats-0.2.0

[ADAM-309] Update to bdg-formats 0.2.0
[ADAM-327] Adding Gene, Transcript, and Exon models