### Please describe the problem.


### What steps will reproduce the problem?


### What version of git-annex are you using? On what operating system?


### Please provide any additional information below.

[[!format sh """
$> mkdir repo; cd repo; git init; git annex init; git annex upgrade; mkdir -p subdir; cd subdir; touch file; git add file
Initialized empty Git repository in /tmp/repo/.git/
init  ok
(recording state in git...)
upgrade (v5 to v6...) ok
git-annex: git: createProcess: runInteractiveProcess: chdir: does not exist (No such file or directory)
error: external filter 'git-annex smudge --clean %f' failed 1
error: external filter 'git-annex smudge --clean %f' failed

$> echo $?; git status
0
git-annex: git: createProcess: runInteractiveProcess: chdir: does not exist (No such file or directory)
error: external filter 'git-annex smudge --clean %f' failed 1
error: external filter 'git-annex smudge --clean %f' failed
On branch master

Initial commit

Changes to be committed:
  (use "git rm --cached <file>..." to unstage)

	new file:   file

$> git commit -m 'added file'
git-annex: git: createProcess: runInteractiveProcess: chdir: does not exist (No such file or directory)

$> echo $?
1

$> git annex version
git-annex version: 6.20180807+git230-gaa291acfe-1~ndall+1

"""]]

also happens with 6.20180807-1  but not with 6.20170101-1+deb9u2, so it is a regression

[[!meta author=yoh]]

> [[fixed|done]] --[[Joey]]
