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The issue is easily described, the daily cronjob causes following mails for me on a CentOS 5.5 machine: /etc/cron.daily/etckeeper: etckeeper warning: hardlinked files could cause problems with git: sysconfig/network-scripts/ifcfg-eth0 sysconfig/networking/devices/ifcfg-eth0 sysconfig/networking/profiles/default/hosts sysconfig/networking/profiles/default/resolv.conf sysconfig/networking/profiles/default/ifcfg-eth0 hosts resolv.conf It seems this issue occurs when the files in /etc/sysconfig/networking/profiles/default are listed. A virtual server I have, also with CentOS 5.5, doesn't send those mails. The files (or rather hard links) in the mentioned directory are missing there. I also do not have this issue with my Fedora installation, the behavior is the same, the hard links in /etc/sysconfig/networking/profiles/default do not exist. Not sure how to handle this, though. Maybe it is some mis-configuration on my CentOS machine or there is some way to avoid those links? Maybe it would be a solution to exclude the files under /etc/sysconfig/networking/ from version control?
Hard linked network configuration files in /etc is quite normal for static network configs on RHEL or Fedora, but will vanish eventually when people use Network Manager only. Discussed a little bit with upstream, but it is not clear yet how to fix that issue. Git simply cannot handle hard links (and also breaks them when updating one of the linked files). That is not something etckeeper can easily simulate in general. For the case of the hard linked network config files though, one could come up with a special script that runs after /etc/etckeeper/pre-commit.d/30store-metadata and records them in /etc/.etckeeper, so they can be restored later. Patches welcome!
Closing for now, unless sb comes up with a good idea how to deal with hardlinks in in Git in general.