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We still have some issues related to packaging.
That's essentially the issue raised at thelounge/thelounge-deb#72
However the issue is persistent over all installation methods and should be fixed in core.
Rather than messing with the filesystem and trying to fix the mess we created we simply warn and let the admins handle it.
While not ideal, at least that solves the issue for new installs and we can always fix it in the packages of the more opinionated packages (read Debian) and maybe warn on do it yourself distros (Arch)