Hi Oliver,

At a minimum, you will probably want to back up the following directories:

        /etc
        /usr/local/etc
        /home

That will get all of the configuration files for FreeBSD and the software thar 
you installed from ports. The last directory will det all of your user's data. 
Some other applications might put data in other places, however, so you might 
want to research the applications that you are running to make sure you don't 
miss any important data.

-Andy.
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