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Why do you think the Kindle does integrity checks on remounting the userstore?
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You can see it doing it if you've jailbroken and installed usbnetwork: do a ps upon remount and you'll see a process whose name I forget pounding away, 100% CPU usage. Check what files it's opening, and look, it's opening every index in turn and flicking through it. (Well, OK, I didn't check that. But it's opening a lot of indexes and walking through each fairly linearly.)