My conclusion in In The Gatekeeper and the Keymaster was that Apple doesn’t plan to offer upgrade pricing in the Mac App Store. Rich Siegel says Apple advises making version 2 a separate app. If that’s the case, Apple should focus on making that model smoother. Right now, unless you offer free updates forever, you eventually have to remove version 1 from the store and add version 2. The user experience for this is terrible. If the store and the OS understood that this is what was happening, there’s so much that it could do to make the process smoother. TUAW commenter chrismcs has a great list of some of the issues.
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