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Cleaning up the whole $HOME/<.pkgname>/ situation for individual app settings
(iusearchlinux.fyi)
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Distributions include the Linux kernel and supporting system software and libraries, many of which are provided by the GNU Project. Many Linux distributions use the word "Linux" in their name, but the Free Software Foundation uses the name GNU/Linux to emphasize the importance of GNU software, causing some controversy.
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Might be worth looking into immutable distros (nix, guix) and their home management systems, or containerised apps (flatpak, where you can inject config). A lot of tools are hardcoded to non standard locations so it's kind of a losing battle by default. A similar strategy would be to use permissions or mount certain folders as read only.
Adding VanillaOS as well, saw it a few days ago and it seems like a pretty decent immutable distro too.