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I have server on ubuntu 22.04/OVH. I have my main files in home. I using docker, and backup every day all docker-compose file and data folder.

I want also backup my server setup, nginx configuration, ssh-key etc, which folder I should add, or maybe backup all partition by clonezilla etc?

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Let the file-hierarchy(7) man page guide you. If this hierarchy is followed, all the settings should be under /etc/. On the other hand, you should never need to backup anything under, e.g., the section "vendor-supplied operating system resources" (/usr/ & /lib/) as they can be reinstalled, nor the section "virtual kernel and API file systems" (/dev/, /proc/ & /sys/).

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