add support for modular file structure

This adds an option to use a modular file structure via options.useModulesStructure"
Not sure if we could have just added the file structure we used as well, but anyway it's more error-prone this way.

PS: I also added karma config to the test watch triggers
done.
my first plan was to use /app directly, such as /app/module1/module1.ctrl.js and so on, but bower comps and other assets that are not module specific will need to be there too, so I preferred to isolate it to modules path.