Currently, all App Store updates are provided free to the user, but in the near future this may change. An example of this is an app which gets a major overhaul such as the Tweetie 1 to Tweetie 2 transformation. Tweetie 2 was a essentially an all-new app so the developers sold at as one not to miss out on the revenue. This is not so streamlined as developers and users alike would be better off if they had the option to update via the normal system, at a cost.
The following screenshot seems to allude to paid App Store updates in the future:
The screenshot seems to dictate that previous users of an app would be able to upgrade at a lower price than a user who is yet to purchase the application at all.
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