Understanding r.js optimizer for whole project

Question

I have a directory structure like this:

assets
  modules
     module1
       models
       templates
       views  //contains individual modules
app.js
build.js
require.js
text.js

And here is my build profile

({
    paths: {
        jquery: 'assets/js/jquery',
        underscore: 'assets/js/underscore',
        Backbone: 'assets/js/backbone',
        bootstrap:'assets/js/bootstrap',
        flexslider:'assets/js/jquery.flexslider',
        fullCalendar:'assets/js/fullcalendar'
    },
    shim: {
        underscore: {
            exports: "_"
        },
        Backbone: {
            deps: ['underscore', 'jquery'],
            exports: "Backbone"
        },
        flexslider:{
            deps:['jquery'],
            exports:"flexslider"
        },
        fullCalendar:{
            deps:['jquery'],
            exports:"fullCalendar"
        }
    },
    baseUrl : "./",
    name: 'app',
    out: "dist/app.js",
    removeCombined: true,
    findNestedDependencies: true
})

When i run the optimizer, I just get one app.js file in dist folder and it doesn't include anything from the modules directory. How do I optimize the whole project? Or i am lacking some fundamental understanding?