[[!comment format=mdwn
 username="joey"
 subject="""comment 2"""
 date="2018-09-11T17:39:05Z"
 content="""
There are a few places in git-annex where it runs git with the cwd
overridden, eg to the top of a git repository.
If it somehow comes up with a path that doesn't exist,
that would explain this error. The most likely one is
in `Git.Config.read'`, which git-annex always runs at startup.

So it probably comes down to git running the clean filter with
the wrong `GIT_DIR` setting or something like that, leading to this as a
cascading failure. And I vaguely remember seeing something like that in the
git commit log, or having dealt with such a problem before.

We could make git-annex upgrade fail to run with too old a git (and it
probably should at least when used with a git too old to support
smudge/clean filters at all!), but it wouldn't help if the repository was
upgraded in a different environment. git is going to run the git-annex via
the clean filter before any check can happen and the most git-annex can
then do is error out somehow.

See also
<http://git-annex.branchable.com/forum/Why_git_commit_fails_from_within_a_newly_git-annexed_subdir__63__/>
which seems to be the same problem without v6; they didn't say what git
version.
"""]]
