The application config should just be in the conf/{appName}/Application.xml. Copy this (and any other custom files in the same directory) to conf/{newAppName}/
You’ll also need to create a folder under applications/ with the same name as the newAppName.
The easiest way is by clicking on the Copy button in the Manager UI. If you navigate to the application page in Manager, there is a “copy” button on the upper right.
Either of those two methods should work. I hope this helps you.