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I'm not positive about this, but it sounds like lots of the applications/utilities made by Many Tricks are going to be pulled, or will at least see slower/limited updates if any: http://manytricks.com/blog/?page_id=2208

TextExpander 4 is one of major examples. TextExpander 3 is still in store but version 4 is only available direct from Smile. There are also ClipStart (I think that's the name, a video management app), SourceTree (version control) and probably some other. More will follow, I believe.

A lot of software can't be sandboxed, full stop. So they joined the App Store before sandboxing even existed, but Apple won't approve any more updates so they will have to be sold outside the store.

I believe Panic with Coda has said the non-MAS version will be getting features that are impossible on the MAS version