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