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The hard part is the user interface, not the backend. The application needs to invoke a privileged UI where the user can choose which files or directories the application may access.

(many storage media are formatted using FAT, so the media API is probably not implemented using Unix permissions)

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I'm talking of allowing apps to mark things (like the WhatsApp data previously mentioned) to only be accessible by itself or some other app(s).

As for FAT, I said in another comment that Google has already imposed MTP on us and Android's adoptable storage uses ext4 anyway, so they could easily require it on all removable storage where application data is stored.

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