NiLuJe has recently posted that 2 consecutive reboots after an update or reset does the trick. Over the years he has also recommended reinstalling hotfix when it has been updated.
A package is anything installed as a kindle update and thus has to be signed. MRPI, KUAL, USBnetworking, KOReader, and screensaver hack are all packages. Non package user addons might or might not get erased by an update. A reset erases all user content.
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