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I'm running FreeBSD, and on FreeBSD most of the packages have their
configurations in /usr/local/etc rather than /etc. (And there's no
/opt
at all.)
The stuff in /etc is config for the OS-included stuff, like the
networking, firewall, DNS, etc. The only thing that I've run into is
that there are variables in /etc that control whether packages are
automatically started at boot (or not). In those cases, you have to
manually retype those variables. (If you look in /usr/local/etc/rc.d
on FreeBSD, you can see all the things that might start at boot --
then you have to manually re-create the entries in /etc/rc.conf -- a
minor pain...)
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