Handle metadata for multiple inputs properly

When there was multiple input directories, it would only generate metadata for one of them. Now, for each input directory, it generates a metadata 'slug'. So rather than:

```js
{
  main: ''
  files: {...}
}
```

it's now

```js
[{
  main: ''
  repo: 'http://...'
  files: {
    './lib/atom.coffee': {}
  }
},{
  main: './lib/text-buffer.coffee'
  repo: 'http://...'
  files: {
    './lib/text-buffer.coffee': {}
  }
}]
```

This way we can generate the metadata for all the includes at the same time and pass that json file to something that creates the intermediate format in one shot.
Guhhhh switching between Ruby and CoffeeScript is going to be the end of me.