I like a lot pacdiff for dealing with pacnew files. I always notice that it miss the grub config because it lies in /boot/ while pacdiff only checks in /etc/ I was curious so I decided to have a look at how many backup config files are not in /etc/ :) $ sh backup.sh > backup-list $ cat backup-list | cut -d'/' -f1 | sort -u boot conf.d home opt srv sysctl.conf usr var Note that we have three crazy files there : empty, conf.d and sysctl.conf. Here are the three problematic files/packages : conf.d/ntp-client.conf / /var/abs/extra/ntp/PKGBUILD /etc/foomatic/filter.conf / /var/abs/testing/foomatic-filters/PKGBUILD sysctl.conf / /var/abs/community/network/ufw/PKGBUILD I should probably report bugs for these, though it was not my original intention. So after this manual filtering, here is the list : boot home opt srv usr var That would considerably slow down pacdiff though so probably not worth it. It is disappointing :)