build.js

({
    appDir: "../js",
    baseUrl: "./",
    dir: "../js-deploy",
    //Comment out the optimize line if you want
    //the code minified by UglifyJS
    optimize: "none",

    paths: {
        'app'                           : 'app', 
        'jquery'                        : 'libs/jquery/jquery-1.7.min',
        'jquery-cookie'                 : 'libs/jquery/jquery.cookie',
        'jquery-dataTables'             : 'libs/jquery/jquery.dataTables.min',
        'jquery-css-animations'         : 'libs/jquery/jquery.animate-enhanced',
        'jquery-parseQuerystring'       : 'libs/jquery/jquery.parseQuerystring',
        'jquery-ui'                     : 'libs/jquery/jquery-ui-1.8.16.custom.min',
        'jquery-isotope'                : 'libs/jquery/jquery.isotope.min',
        'jquery-tipsy'                  : 'libs/jquery/jquery.tipsy',
        'jquery-ajaxmanager'            : 'libs/jquery/jquery.ajaxmanager',
        'jquery-form'                   : 'libs/jquery/jquery.form',
        'chosen'                        : 'libs/jquery/chosen',
        'util'                          : 'libs/rap/util',
        'loading'                       : 'libs/rap/loading',
        'date'                          : 'libs/rap/date',
        'log'                           : 'libs/rap/log',
        'underscore'                    : 'vendor/underscore',
        'backbone'                      : 'vendor/backbone',
        'visualsearch'                  : 'libs/backbone/visualsearch',
        'templates'                     : 'templates/templates',
        'moment'                        : 'libs/moment/moment.min'
    },

    modules: [
        {
            name: "plugins"
        },
        //Optimize the application files.
        {
            name: "main",
            exclude: [
                "plugins"
            ]
        }
    ]
})

index.html

    <script data-main="js/main" src="js/libs/require/require.js" type="text/javascript" charset="utf-8"></script>
    <script>
        require.config({
            paths: {
                'jquery'                        : 'libs/jquery/jquery-1.7.min',
                'jquery-cookie'                 : 'libs/jquery/jquery.cookie',
                'jquery-dataTables'             : 'libs/jquery/jquery.dataTables.min',
                'jquery-css-animations'         : 'libs/jquery/jquery.animate-enhanced',
                'jquery-parseQuerystring'       : 'libs/jquery/jquery.parseQuerystring',
                'jquery-ui'                     : 'libs/jquery/jquery-ui-1.8.16.custom.min',
                'jquery-isotope'                : 'libs/jquery/jquery.isotope.min',
                'jquery-tipsy'                  : 'libs/jquery/jquery.tipsy',
                'jquery-ajaxmanager'            : 'libs/jquery/jquery.ajaxmanager',
                'jquery-form'                   : 'libs/jquery/jquery.form',
                'chosen'                        : 'libs/jquery/chosen',
                'util'                          : 'libs/rapsphere/util',
                'loading'                       : 'libs/rapsphere/loading',
                'log'                           : 'libs/rapsphere/log',
                'gmaps'                         : 'libs/rapsphere/gmaps',
                'underscore'                    : 'vendor/underscore',
                'backbone'                      : 'vendor/backbone',
                'visualsearch'                  : 'libs/backbone/visualsearch',
                'templates'                     : 'templates/templates',
                'moment'                        : 'libs/moment/moment.min'
            },
            priority: [
                'jquery',
                'underscore'
            ]
        });
    </script>

main.js

require(['backbone', 'router', 'router/appRouter', 'router/deviceRouter', 'router/userRouter', 'widgets/globalSearch', 'loading', 'plugins'],

plugins.js

/**
 * Bundle of all the plugins.
 */
define([
    'jquery',
    'date',
    'jquery-cookie',
    'jquery-dataTables',
    'jquery-css-animations',
    'jquery-ui',
    'jquery-tipsy',
    'jquery-ajaxmanager',
    'jquery-form',
    'chosen'
], function() {});