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Smile Software (PDFPen) adopted the approach of selling a little app for the minimum price in the Mac App Store that allows a customer who bought the main app from them directly to get/put documents into iCloud. Somewhat less convenient to use, I'm sure, but they are still free to do things in the main app that run afoul of Apple's rules. It's not impossible to imagine some of Apple's desired security improvements making some of the integration and scripting features off-limits to Mac App Store applications.