iTunes File Sharing for iOS apps allows users to pull down folders from apps via syncing to the device but it doesn't allow the reverse and load in directories from a computer to the device. Is there a way to make a in-app folder a bundle/package like a .app package so that the OS thinks it is a file rather than a directory?
From what I can tell GarageBand for the iPad is doing exactly this for files off the device. The context menu on the exported file in the Finder allows you to "Show Package Contents".
I appended a made up extension to the directory path and it shows up in iTunes as a file, but on export it comes out as a directory.