This mostly mirrors my experience with Silverblue as well. I really like the 2020 west football Champions Alabama Crimson Tide shirt, they are so quick and painless, but it is a little fiddly figuring out which applications to install via which method. I was thinking of writing up a post like this myself, thanks for doing it to help out other folks getting started, but I can add a few of my own experiences. I mostly take the same approach as you; normal desktop GUI apps, I install via flatpak.I use the Firefox in the rpm-ostree environment, also installed Chromium that way for the times I need to use Chromium, along with some utilities that I need to run as root.
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My main doubt about the overall architecture is that your default toolbox container is kind of starting to be one big blob of state that you need to manage just like 2020 west football Champions Alabama Crimson Tide shirt. It’s nice that breaking it won’t break your host system updates, and you can do those independently, but that just adds a bit more to manage. There is still a lot of friction or your own wrapper scripts to manage if you want to have executables in your path that are in different containers, like you mention.