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.