The problem I’m having with this is that slackpkg clean-system shows all packages I’ve installed with slackpkg+ from other repos to be removed, too.
But if I blacklist them, they won’t get updated either.
Is it even necessary to run those commands on a normal update, or do packages only get added/removed in a new release?
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Not clean-system. But yes on install-new.
I think there are different functions to the commands you cited.
install-new seek for new uninstalled software in the system
clean-system will remove the packages that is not contained in the list file from your repository. upgrade-all is the command to upgrade existing packages and not mess with the others.