Fixes #484 - adds application.js and formats JS

- Adds application.js, which is a module attached to all views.
- Moves domReady! plugin to application.js
- Removes the .require-loaded class because tests no longer look for
this class.
- Performs JS dependency array and code comment formatting to make the
modules more consistent in syntax with each other.
Fixes #465 - Adds additional RequireJS docs

- Adds JS configuration comments to installation customization
instructions.
- Adds code comments to requirejs.yml