flatkill.org is clickbait, not written in good faith, and doesn't propose any solution. Moreover things like "it's obvious Red Hat developers working on flatpak do not care about security" is just unnecessary and toxic.
Issues mentioned on flatkill are already fixed, will be fixed or doesn't depend on flatpak itself (like the UI / icon in the software app store).
I don't like Flatpak either but I think we should elevate the debate to deeper architectural issues of flatpak that won't be fixed easily. Personally, I do not like the following in Flatpak :
- no effort on full reproducibility like Nix&Guix
- a big fat flat runtime rather than traditional fine grained dependencies (although OStree avoids duplication, but still very elegant)
- you can't install extra pkg in the sandbox. So the quite overkill solution in RedHat's vision is to separate between Toolbox/Podman for devs vs Flatpak for users, rather than trying to make a single unified sandbox for everything. Of course everything breaks down when you try to code using a Flatpaked IDE, if you follow RedHat's vision you basically need to spawn a toolbox container from an unsandboxed flatpak instance of your IDE :
https://github.com/flathub/com.visualstudio.code/issues/44
So personally, I'm still waiting for a packaging system that is :
- compatible with the idea of a declarative/immutable os (like nix, guix, silverblue)
- tries to make everything reproducible (like guix)
- sandboxed with runtime permission API (like Flatpak portals, IOS, Android)
- sandbox can be augmented with packages so that you can code in your sandboxed IDE + add necessary dev packages inside a same sandbox without having to break it