These following javascript files are the original, hand-written javascript files.

app/assets/js/master/*.js

These masters are deprecated since Coffeescript is now used generate the Javascript.
The master CoffeeScript files are in:

src/coffee/ 

Developers should use command line to watch and generate the javascript builds:

app/assets/js/build/*.js

On background, running terminal window use the following command line:

coffee -c -b -o ./js/build -w ./coffee

To manually build and deploy the application code, developers can use the cake file:

cd src cake deploy