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
should be `{app,.tmp}/`so we can support haml and typescript. why do we need the `modules/`?