support for using a custom modules dir for third party modules

I've added support for passing a `root` relative `dir` for looking up third party modules ala `node_modules` style as [explained here](https://github.com/michaelficarra/commonjs-everywhere/issues/106)

Command Line Usage

```bash
cjsifiy app.js --root js/ --modules-dir components/ 
```

Node Usage

```js
cjsify ( './app.js', __dirname + '/js', { modulesDir : './components' } );
```

The docs have also been updated.