Generate documentation for protected methods.

Some important method documentation as [send_devise_notification](https://github.com/plataformatec/devise/blob/master/lib/devise/models/authenticatable.rb#L130) is not
being generated.

This configuration file will customize documentation to include
protected methods and should work with rubydoc.info.

I've also added the embed-mixin option, that is not currently working
because yard cannot identify them correctly, but it should simplify
documentation a lot once someone can fix it.