[[!comment format=mdwn
 username="joey"
 subject="""comment 5"""
 date="2021-01-21T18:14:09Z"
 content="""
Thanks Mike, that confirms it's failing to unset the config that's not set.

The .git symlink is what git-annex is supposed to set up, so it should not
need to do anything else and the question is, why does it still think it 
needs to change something?

I was able to reproduce the warning, just run `git submodule add foo
/path/to/annexrepo` and then in foo, `git-annex init` and then it
happens part-way through. Due to two different git-annex processes both
trying to do the same conversion, with the second one failing.
I've fixed that. 

My fix will also fix your problem. But, I don't actually
understand how to reproduce your problem. I was only able to make it happen
when running `git-annex init` (or letting it auto-init), 
not running other git-annex commands in a repo it's already initialized.

Maybe you have `GIT_DIR` set to "../../../.git/modules/..."?
"""]]
