browser.html

<script src="mootools.js"></script>
<script>

Moo.apply(this); // For non-strict browsers
Moo.apply(window); // For strict browsers

</script>

commonjs_app.js

// CommonJS
var Moo = require('mootools');

Moo.apply(this); // For most CommonJS implementations


// For strict CommonJS implementations
Moo.apply({
	String:String
});
var Class = Moo.Class;


// For exported sandboxed natives support
//   without breaking scripts in a normal context
//   you wouldn't be able to use literals without a *.from() wrapped around it
(function(context, Array, Date/*, etc…*/){
	
	var myArray = Array.from([1,2,3]);
	
	var myString = String.from("abc");
	
	var MyClass = new this.Class({
	});
	
}).apply(MooTools, MooTools.natives);
// MooTools.natives is an array of [context, Array, Date, etc…]

MooTools.js

// Wrap all of MooTools code in a function
/*<b support="CommonJS Modules namespace">*/var MooTools = function(exports){/*</b>*/
	
	// fallback exports to `this` so that it can be used as both:
	// `MooTools.apply(context)`
	//   this is the only style that'll work in CommonJS since exports can't be a function
	// `MooTools(context)`
	// `MooTools()`
	if (typeof exports == 'undefined') exports = this;
	var context = exports;
	
	
	// changed `this.Whatever = …` to `exports.Whatever = …` to be more explicit what is being exported
	var Class = exports.Class = function(){};
	
	
	// All natives must have `exports` prepended for sandboxed scope support
	context.String.prototype.foo = function(){ return "foo'd"; };
	
	
	// Return the exports object for namespaced use
	return exports;
	
/*<b support="CommonJS Modules namespace">*/};/*</b>*/

/*<b support="CommonJS Modules namespace">*/// Create the exports object unless it exists
	if (typeof exports == 'undefined') exports = {};
/*</b>*/

/*<b support="CommonJS Modules">*/
	// Create an apply method that will work in CommonJS
	//   since exports can't be a function
	exports.apply = function(context, args){
		return MooTools.apply(context);
	};
/*</b>*/

/*<b support="namespace">*/
	// add all natives to exports
	exports.Array    = Array;
	exports.Boolean  = Boolean;
	exports.Date     = Date;
	exports.Function = Function;
	exports.Number   = Number;
	exports.Object   = Object;
	exports.RegExp   = RegExp;
	exports.String   = String;
	
	// add some host objects to exports
	if (typeof Element != 'undefined') exports.Element = Element;
	
	// extend exports itself with MooTools for namespaced use
	exports.apply(MooTools);
/*</b>*/