storing things "in apps" still makes a file on a filesystem, but it's less reliable and the user doesn't know where it is
Files are currently used to implement apps, but that can be seen as a transitional measure, like an OS that supports both files and raw disk access. A fully app-based OS without files, though not existing currently, would be possible.
Another idea the industry discarded was to make the disk a big SQL database, again without files.