Please check this, since it is probably an issue with the implementation for
this particular VCS, which removes empty directories.
I think the bug should get forwarded to upstream (Debian), since they/he
probably know where to fix it it from the top of their/his head(s).
** Changed in: etckeeper (Ubuntu)
Status: Incomplete => Triaged
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etckeeper deletes empty directories on apt-get upgrade
https://bugs.launchpad.net/bugs/305642
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