That is not very good.
Suppose you create an audio file with Audacity and a series of images with ImageMagick and GIMP, then use ffmpeg to combine them into a video and VLC to view it. They're all operating on the same files.
What we need is to add an application list to filesystem ACLs and then have security groups like Video and Finances which contain apps. Because GIMP should be able to access your photos but not your accounting spreadsheet.
It should even be possible to do some of this automatically by file type, e.g. GIMP can access any PNG file the user can but not any spreadsheet file, or read a shared library but not write to it.
Does anything remotely resembling this already exist?
Edit: Before anyone says that SELinux resembles this, as far as I'm aware SELinux policies are anything but simple to set up and use correctly. However, SELinux types are inherited from parent directories and do look an awful lot like this. The main thing missing would seem to be that I can't find how to apply multiple contexts or types to a single file, but perhaps I'm just failing to navigate the manual?
This isn't that hard in a technical sense. But I very much doubt you can get the casual users to actually do that. They'll just end up with one giant group, because it's the easiest and doesn't require understanding the concept of security boundaries.
Basically, it'd be Vista UAC prompts all over again.
It is more cumbersome to use than the current mainstream paradigm, but not that much!
Of course, it is silly to sandbox your bread-winning software. I don't sandbox Android Studio. Or ffmpeg. Or VLC. Personally, I believe that nobody has a right to decide, how to sandbox software on other people's computers. I think, that such decision should be left to users of that software. Unfortunately, it looks like Flatpak does not make that easy.
I stopped using desktop Linux a long time ago and now use a Mac for my desktop work. I take things a bit further and don't let anything write to my $HOME/Desktop -- it's read-only. I don't recommend that as a default for anyone either!
But as far as Flatpak, a few of the "featured" apps are things like Inkscape, Gimp, VLC, or LibreOffice. Not apps that you'd really want to sandbox isolate like you described. (And as you mentioned -- you wouldn't want to do that anyway).
Now a few of the others were Spotify and Slack. Things that you could (should?) definitely sandbox.
I guess I don't see the point in having applications (that is intended for a general purpose user) that (a) need access to your home directory to read/write files and (b) should only have access to a sandboxed pseudo-home directory. Either sandbox it so it doesn't have $HOME access at all, or don't. I'm not sure I see the benefit to this middle ground. Especially for the use-case of general user desktop applications. For server applications, I could potentially see the benefit (although, containers have probably already filled this scenario). What is the use-case you're thinking of?
I appreciate your point of view that no one should be able to decided for you how to sandbox software, but no one is forcing you to use Flatpak packaged programs[1]. Perhaps there should be some way to re-build a Manifest that limits access, or make it so that you can more easily switch granted privileges -- that would probably be a good thing. But someone has to set defaults. If a Flatpak packaged program has too liberal defaults, then maybe that's best treated like a bug and hopefully there is a mechanism to send a patch.
[1] yet... but it might be coming. I think the only way you'd see commercial applications like Photoshop for desktop Linux would be wrapped in something like Flatpak. I still think that most open-source applications will still be packaged by the main distro repositories, regardless of how well Flatpak does.
I'm curious how you do this? What's your setup?
I don't use Flatpak etc. — all of my jails use system-wide libraries and executables. They are just launched inside sandbox environment.
I have been using a directory-per-program sandboxing setup for several years (and still do). It is very convenient, and does not require any additional effort to adapt. In fact, I now have less clutter in my actual $HOME than ever before.
Programmers like to come up with clever ways to solve nonexisting problems. I say — give user a way to bootstrap a sandboxed environment into a directory of their choice (no, using auto-generated directory names is NOT allowed!), and the "problem" would no longer exist.