The 2 previous postings were about getting the native apps up and running for their respective Android and iOS environments. The official guide takes you to a Hello World index.html which merely displays a static message. In reality, the app that your user will interact with is the UI of the index.html or the HTML5 app. The underlying native app that runs the index.html is what I call a Shell Native App.
So, the actual primary app is a HTML5 file with various supporting web libraries to fulfill the functions of a full-fledged mobile app. Generally, it should have the following supporting technologies to give it the native look and feel and experience:
1) jQuery (www.jquery.com)
2) AJAX (With AJAX, our mobile application can send data to and retrieve data from a server asynchronously (in the background) without interfering with the UI experience of the existing page.)
3a) jQTouch (www.jqtouch.com)
3b) jQuerymobile (www.jquerymobile.com)
As for the Shell Native Apps, they host the app icon, the splash screen, PhoneGap libraries and other native information. If you require certain native functions, it is inevitable that you will need to modify the natives codes for your Shell Native Apps. A good example would be the implementation of Push Notifications for both iOS and Android, you are unable to do this in the HTML5 app, which means you have to put in codes in your Shell Native App.