Rolf, I had this issue too. The problem is that etckeeper updates the
.etckeeper file in a pre-commit hook (this file is necessary because git
does not store the owner and permissions directly).

When you are rebasing, somehow the pre-commit hook interacts badly with
the rebase. However, its quite easy to fix: when a rebased commit shows
a conflict in .etckeeper, simply do:

etckeeper pre-commit

This will run the pre-commit hook explicitly and update the .etckeeper
file for the current commit, and then rebase --continue will work fine.

Some relevant information about why the etckeeper pre-commit hook may be
giving weird results / conflicts with the rebase:

http://git.661346.n2.nabble.com/rebase-i-reword-runs-pre-commit-hook-
with-curious-results-td7244648.html

I also posted a question on
https://joeyh.name/code/etckeeper/discussion/ about this.

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https://bugs.launchpad.net/bugs/1095181

Title:
  terrible breakage on git rebase

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