Comment 5 for bug 305642

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Daniel Hahler (blueyed) wrote : Re: etckeeper deletes empty directories on apt-get upgrade

I did not meant that you should forward the issue, but only stated that it should be done.

As documented, git cannot track empty directories and therefore this extra metadata should get stored in /etc/.etckeeper.
Please provide the output of
  sudo grep -E 'mkdir|mysql' /etc/.etckeeper
There it should be stored that /etc/mysql.d needs to get created.

You could also track the history of this meta file, e.g. by using "sudo git log /etc/.etckeeper" and find out, why /etc/mysql.d has been removed from it (or if it has ever been added).
There should be graphical browsers for Git, but I don't know any from the top of my head.