`GIT_DIR` support isn't right. Git does not look for `GIT_DIR/.git`; git-annex does. Also, to support this scenario, support for core.worktree needs to be added as well: mkdir repo workdir git --work-tree=$PWD/workdir --git-dir=$PWD/repo init export GIT_DIR=$PWD/repo git status # ok git annex init "new repo" # fail --[[Joey]] > [[fixed|done]] --[[Joey]]