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:
src/
All source code (further breakdown should happen in this folder (plugins folder / etc, but will be handled in another task
pkg/
The build output
docs/
All supporting documentation (samples / etc)
tests/
Unit test code.
build/
Any build support code, test runners, test markup, etc.
thirdparty/ or lib/
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.