Directory Structure

app.build.js

({
	appDir: '../',

	baseUrl: '../js/',

	dir: '../../Website-build',

	//optimize: 'none',

	paths: {
		'shared-libs': '../libs/shared-libs',
		'map-libs': '../libs/map-libs',
		'main': 'map/main'
	},

	modules: [
		{
			name: 'shared-libs'
		},
		{
			name: 'map-libs'
		},
		{
			name: 'main',
			exclude: [
				'shared-libs',
				'map-libs'
			]
		}
	]
})

gistfile1.txt

/
    /build
        app.build.js
    /js
        /map
            main.js (when built will contain all dependencies)
    /libs
        /jquery
            jquery.1.7.1.js
        /...(other libs here in subfolders
        map-libs.js (dummy file that will contain all the compressed map libs)
        shared-libs.js (dummy file that will contain all the compressed shared libs)

main.js

require.config({
	priority: ['../libs/shared-libs', '../libs/map-libs', 'main'],

	paths: {
		//libraries
		'jquery': '../../libs/jquery/jquery-1.7.1.min',
		'underscore': '../../libs/underscore/underscore-min',
		'backbone': '../../libs/backbone/backbone-min',
		'bootstrap': '../../libs/bootstrap/bootstrap.min',
		'bootstrap-datepicker': '../../libs/bootstrap/bootstrap-datepicker',
		'date': '../../libs/date/date',

		//map libraries
		'leaflet': '../../libs/leaflet/leaflet-src',
		'iconlabel': '../../libs/leaflet/plugins/Icon.Label',
		'wax': '../../libs/wax/wax.leaf.min',

		//require plugins
		'text': '../../libs/require/text',
		'use': '../../libs/require/use',
		'order': '../../libs/require/order',

		//jquery plugins
		'color': '../../libs/jquery/plugins/jquery.color', //should we remove this, it is 16KB??
		'limitmaxlength': '../../libs/jquery/plugins/jquery.limitmaxlength',
		'smartresize': '../../libs/jquery/plugins/jquery.smartresize',
		'autocomplete': '../../libs/jquery/plugins/jquery-ui.autocomplete.min', //temp until bootstrap typeahead supports remote datasources
		'timepicker': '../../libs/jquery/plugins/jquery.timeentry'
	},

	use: {
		underscore: {
			attach: '_'
		},
		backbone: {
			deps: ['use!underscore', 'jquery'],
			attach: function (_, $) {
				return Backbone;
			}
		},
		bootstrap: {
			deps: ['jquery']
		},
		'bootstrap-datepicker': {
			deps: ['jquery', 'use!bootstrap']
		},
		leaflet: {
			attach: 'L'
		},
		iconlabel: {
			deps: ['use!leaflet']
		},
		wax: {
			deps: ['use!leaflet'],
			attach: function (L) {
				return wax;
			}
		},
		color: {
			deps: ['jquery']
		},
		limitmaxlength: {
			deps: ['jquery']
		},
		smartresize: {
			deps: ['jquery']
		},
		autocomplete: {
			deps: ['jquery']
		},
		timepicker: {
			deps: ['jquery']
		}
	}
});

require([
	'jquery',
	'use!leaflet',
	'router',
	'collections/Resources',
	'models/UserSettings',
	'views/Application'
	], function (jQuery, L, Router, Resources, UserSettings, Application) {
	jQuery(/function ($) {
		//...
	});	
});

map-libs.js

define(["leaflet", "iconlabel", "wax"],
function () {
    //Just an empty function, this is a place holder
    //module that will be optimized to include the
    //common depenendencies listed in this module's dependency array.
});

shared-libs.js

define([
	'jquery',
	'underscore',
	'backbone',
	'bootstrap',
	'bootstrap-datepicker',
	'date',
	'leaflet',
	'iconlabel',
	'wax',
	'text',
	'use',
	'order',
	'color',
	'limitmaxlength',
	'smartresize',
	'autocomplete',
	'timepicker'
	],
	function () {
		//Just an empty function, this is a place holder
		//module that will be optimized to include the
		//common depenendencies listed in this module's dependency array.
	}
);