> These packages also make it hard to audit the versions of security-critical code installed on my system.

I think someone else has mentioned this somewhere, but Flatpak exposes information about the runtime it's using -- you can use metadata tools to iterate over the packages installed and check to see if any of them are outdated. I suppose the tooling in that area could be improved, but I suspect that's something that would happen in parallel with more maintainers getting involved in validating/moderating packages. I could easily see a world where you specify a set of minimum runtime versions (or pin an exact runtime version) and set up some rules about what packages you'll allow to run.

Importantly, if you do have a critical vulnerability, you can make a list of the packages in your system that would be affected, and if you're willing to re-bundle them you can update the runtime for just them, which means if you're a maintainer you can push that update out immediately for those programs to everyone; you don't have to wait until somebody has finished checking to see if the update breaks a calculator app that doesn't have Internet or file access anyway.

I don't think there's anything about Flatpak that blocks this kind of auditing (and the core technology may end up making it easier in the long run). So I do get the criticism, but it seems like the criticism here is more, "we need some more focus given to better userland tools" and not "this is the wrong technical/architectural direction to go."

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> at least when apt-get was upgrading shared libraries, I could be sure that all programs had the fix

Ironically, this is kind of the same behavior that the linked article calls out. You really couldn't be sure about that back then. Plenty of packages embed critical libraries like libsodium and don't use the shared versions. It is very common advice in the Linux world (particularly with games) to embed as many system libraries as reasonably possible, and regardless of whether or not that's good advice, developers do it.

So right now, you're trusting package maintainers to catch that stuff and make sure that the dependencies are updated across the board (or converted into calls to shared libraries) even if the source code isn't using shared libraries by default. And after Flatpak, you'll still to some degree be trusting maintainers to do that, and you'll still be trusting maintainers to say that "updating libsodium" means updating every package that depends on it. The difference with Flatpak is that this is now very explicit and obvious to you, which may be a good thing because (in the article's words) it seems that the single shared runtime model "leads people to place more trust than they should" in their ability to ensure that applications are actually using system libraries.

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> but the waste of space still bothers me

I don't have too much to say here, it's a legit worry.

I think this mostly comes down to how much space will actually be wasted in practice. Docker seems to be relatively inefficient about this, I'm not sure if Flatpak is better or not. But yeah, it would be good to minimize size as much as possible, I do understand that concern.