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Cleaning up the whole $HOME/<.pkgname>/ situation for individual app settings
(iusearchlinux.fyi)
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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.
Yeah, Nix(OS) with Home-Manager is great for managing dotfiles. Impermanence is also nice but a bit more complicated.
Adding VanillaOS as well, saw it a few days ago and it seems like a pretty decent immutable distro too.