The problem could be that name and email are not configured in git for
the root login. To do it you can do following:
sudo -s
git config --global user.email "y...@example.com"
git config --global user.name "Your Name"
Can you please check if this solves your problem?
Another problem exists with the update manager, which still fails when
name and email are set for root (#1335391).
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https://bugs.launchpad.net/bugs/1267564
Title:
etckeeper with git breaks package upgrades that touch /etc
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