I’m selling TaskPaper both from from TaskPaper.com the from the Mac App Store. Generally the two versions are exactly the same. There are the differences that I’m aware of:
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The Mac App Store version is Sandboxed (a security technology required of all Mac App Store apps) while the direct download version is not. For most use cases this should make little difference.
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The Mac App Store version updates may be a bit delayed as they must pass through the app store approval process. To date this hasn’t proved much of a delay for TaskPaper.
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The Mac App Store version supports iCloud directly. The version from my website will not… only apps sold through Mac App Store can support iCloud directly. Either version can save documents to iCloud Drive.