[ADAM-335] Updated README.md to reflect migration to appassembler.
Merge pull request #337 from fnothaft/appassembler-update-docs

[ADAM-335] Updated README.md to reflect migration to appassembler.
[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