> Is the core the database(the filesystem) and the apps roam around in it, or is the core the apps each with their own database.
The first option is evidently better for the user. The filesystem is a neutral entity with a well-defined interface, whereas each app is on its own journey. For a period of time that journey may align with the user's workflow, and both are happy. But there inevitably comes a time where the app and the user diverge, and for the user, it is imperative that they be able to switch to another app without losing access to their data.
To a user, the data matters most, and the filesystem, because of its neutrality, is the best model for access.
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.
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.