Support 'paths' option

I probably do something wrong, but I'm building a webpack application (classic CommonJS app), and documentationjs seems to stop at the main.js without resolving the required modules.

```
'use strict';

var App = require('app/app');

/**
* Main module - App entry point
* @module Main
*/

var Main = function(){};

/**
* Callback fired once the document is ready
* @public
*/
Main.prototype.onReady = function() {
var app = new App();
app.init();
}

var main = module.exports = new Main();
```

What do I do wrong? Thanks!