By default, software has a sandboxed location that is exposed to the host in `~/.var/app/[APP]`.

Most software needs access to user files. Since most applications aren't written with Flatpak in mind, they will attempt to load files using their own file browser, meaning that for the application to function at all it needs to have access to swaths of extra data. You can see what data the application can access either via FlatSeal or in whatever "app store" you're using. Often it'll be your entire home directory.

The software that is designed with Flatpak in mind will use XDG Desktop Portals, where the host displays a file browser and then hooks it up to the sandboxed app so it has access only to that file or directory.

Note that you can't magic your way out of this. You can't eg. wait for the program to request access to a file before displaying a "Program wants access to this file. Allow/Deny" because the program doesn't know if this file exists, and the user wouldn't be able to navigate to it via the program's bespoke file browser since it doesn't have access to directories or their contents.

It's up to you, really, to only use flatpaks that declare tight permissions and implement the proper protocols to safely access resources they don't declare.

This isn't always easy and a lot of software on flathub is old-ish, so people tend to open up permissions since it's difficult to implement all these features properly. In my experience people will rarely stand in your way if you try to improve a package.

> But I would much prefer a "An application is a directory and by default cannot access anything outside of that directory" approach.

That makes sense if the application is the only program that needs to interact with the data. For example: If you have a drawing or photo editing program. You might have downloaded an image from the internet or from your camera. Then you make some edits. Afterwards you want to send the image to someone else via e-mail, which is another program.

Same prefer, although I'm not sure what you mean by "installing changes data in places on my disk"?

Nothing should change, all installations and addons go to the ~/.var directory. When you launch the application, yes it can start reading and writing to arbitrary places on disk, which is why I make it a habit of first launching Flatseal to modify permissions and know exactly what it can and can't do and reach.

I actually vastly prefer this methodology with what we have right now, but if it or something else adopted an application/directory methodology as you described I'd be elated.

Isn't that exactly how it's supposed to work, though? When I install a flatpak app for my user, it gets put into a standard location as a directory and by default has no access to filesystem other than the apps own config and data dirs (can't remember the paths). The fact that many apps choose to require excess permissions and can then bypass standard locations is a different matter

I'd prefer that too. Preferrably with permission popups for requesting folder access outside of it. Shared libraries / whatever flatpak calls them could live at a central symlinked location?

Tech debt, primarily. Flatpak is designed to be able to package apps not designed with it in mind.

If neither compatibility nor resources are of concern then integrating true Mandatory Access Control into both the UX and the entire tech stack would be the best way forward.

I use podman for things like this, works perfect until you want desktop applications but you can hack it about a bit to work fine with pipewire and Xephyr and you have. I feel like a lot of these desktop container systems are horrible and are quite hostile to configuring in the way you want around permissions and such and podman or docker does a better job.