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I'm not talking about the server, since you can run your OWN server if you need to. I was specifically referring to the iOS device that was running OmniFocus.

The "iOS Data Protection APIs" are important for making sure that the full force of on-device encryption is applied to the data stored by a particular program. Aside from Mail, very little of what's on an iPhone/iPad/iPod touch is protected with that full level of encryption.