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Thanks! Yeah I have only a few changes to /etc and /opt. So I will need to reinstall everything in the end? Or just things that install into / rather than /home for some reason?
The exact structure can be different with different distros. When I used arch a decade ago, all config basically went into /etc/rc.conf IIRC, debian/Ubuntu never did that. I don't know pop OS and haven't used kubuntu in a while, so I can't say anything about that. Just be aware that you may have to redo some configuration. Also, you will have to reinstall basically everything except for some wine apps or so that are stored in /home