Allow passing streams to module pack pipeline

This PR allows us changing the file tree before compiling. Here is the way I use it;

```js
b.plugin(function (b) {
     var pack = b.pack;

     b.pack = function (opts) {
       opts.sourceTransform = through(function (row) {
         // change the row
         this.queue(row);
       });

       return pack.call(this, opts);
     };
});
```