Unlike in vanilla Cordova projects, custom plugins are configured in the cloud: http://guides.appgyver.com/steroids/guides/cloud_services/plugin-config/
You still need to include the correct JavaScript files manually – the <asset> tag is currently unsupported.
For verified plguins and JavaScript files for the plugins included with AppGyver Scanner, see the GitHub repo at https://github.com/AppGyver/steroids-plugins