Why not just use the XCode organiser (via AppleScript if you want automation) to delete applications or download/upload app sandboxes? There's no need to touch the phone or use "iFunBox" for this.
The Xcode also only shows a subset of applications. My particular use case is that other developers have written apps using a library that I have authored. I then update the behaviour of the library for their needs based on interactions between the app and configuration for the library.