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The pkgsrc package database, which by default lives in /var/db/pkg/, should not be there. Instead, it should be under /usr/pkg/libdata/pkgdb/. The same applies to FreeBSD's and OpenBSD's ports and also Debian's dpkg, but I'll focus on pkgsrc because it's the system I know best. Let's see why the current default is suboptimal and why libdata is a good alternative.
The scripts that live under /etc/rc.d/ in FreeBSD, NetBSD, and OpenBSD are in the wrong place. They all should live in /libexec/rc.d/ because they are code, not configuration. Let's look at the history of these systems to see how we got here, why this is problematic, and how things would look like in a better world.