Current code needs some reorganization as it is confusing where everything lives and the root dirctory is a flood of files that all server different purpuses.
Top level directories should be created to sort files into logical groupings:
All source code (further breakdown should happen in this folder (plugins folder / etc, but will be handled in another task
The build output
All supporting documentation (samples / etc)
Unit test code.
Any build support code, test runners, test markup, etc.
Third party code (jWorkflow, jasmine, etc) that is needed for building / bundling / etc
root dir should really only include the JakeFile, README.md, license information.
I like that.