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But that leads to a thing where an app has a file format that contains a bunch of its data, and it acts like a mini-database anyway, except now the user needs to remember where it is located. Then if there's data that links between multiple files and doesn't belong to a particular one, it is blurred again.

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Yup it's not perfect, but in the filesystem model, the file continues to exist until an alternative solution emerges. In the app model, the file (and associated data) may be locked away forever.

These are all relatively trivial problems, or (in the last case) essential risks of increased power.

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