[ADAM-332] Upgrades ADAM to Spark 1.0.1.
Merge pull request #333 from fnothaft/upgrade-spark

[ADAM-332] Upgrades ADAM to Spark 1.0.1.
[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