Moves the code from js/config/marionette/application.js into two utility files

This is because the code in that file is application specific and so it
doesn’t belong to the config directory that contains general
configuration
Deletes the js/config/javascript.js file

This is not even used in our application
Renames Controllers.Base to Controllers.Application
Minor modifications in the js/backbone/lib/controllers/application.js

Just like in Ruby calling super with no arguments in coffee script
automatically passes the arguments along.