Layering packages in Fedora Silverblue is not strictly forbidden, but it should be considered the last resort.

For example, I prefer to layer the ZSH shell:

Note that you must reboot when you layer packages.

Quoting from the documentation:

Using package layering creates a new deployment, or bootable filesystem root. It does not affect your current root. This preserves rollback and the transactional model, but means that the system must be rebooted after a package has been layered or updated. You can alternatively use rpm-ostree install --apply-live <package-name> to also temporarily apply the change directly to your currently booted deployment. It’s generally expected that you use package layering sparingly, and use Flatpak and Toolbx whenever possible.

After rebooting, we can verify that ZSH is correctly installed and it’s also reported as part of the current image:

Here I show the packages I layer.

Before that, I need to add external repositories for:

• Visual Studio Code, because the flatpak version is too sandboxed and I’m not willing to spend time on further configuration without further benefits
• Dropbox, because the flatpak version breaks now and then (actually, too often for my taste)

And then I run

In particular,

• gcc is required for tree-sitter-cli and neovim installation via Homebrew.
• the two gnome applications are not available as flatpaks
• I prefer having the JDK (my most used application being Java, my main programming language) as a system package, especially to have Eclipse pick it automatically