Phonegap is creating a native app based on the static html pages is fetches from your website, so if you need to update\change anything in the app logic and structure - you will need to publish a new version, just like a regular native app would work. Webview is actually a container that works with your back-end webserver all the time, so whenver the changes are made on the webserver - it is applied seamlessly to your application, without the need to redeploy.