[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

@tdanford: I don't know how the jc_adam.fgenotype file was created (as there was no jc.vcf file), so I've ignored the test and deleted the file. If you have that file, I can convert it and include that test again.
Nit: order scala after org