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git-annex does not take into account the --git-dir and --work-tree command line options (while they can be useful when scripting).
> mkdir /tmp/test
> cd /tmp/test
> git init
Initialized empty Git repository in /tmp/test/.git/
> git annex init test
init test ok
> touch foo
> cd
> git --git-dir=/tmp/test/.git --work-tree=/tmp/test annex add foo
git-annex: Not in a git repository.
regular git add works:
> git --git-dir=/tmp/test/.git --work-tree=/tmp/test add foo
> git --git-dir=/tmp/test/.git --work-tree=/tmp/test status
# On branch master
#
# Initial commit
#
# Changes to be committed:
# (use "git rm --cached <file>..." to unstage)
#
# new file: foo
#
git-annex version: 3.20110702
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