### Please describe the problem.
The way git-annex deals with submodules (replacing the .git file in the submodule, with a link to the corresponding gitdir of the submodule) seems to confuse Git when creating another submodule in an annex-init'ed submodule.

### What steps will reproduce the problem?
    % mkdir some ; cd some; git init
    Initialized empty Git repository in /tmp/some/.git/
    % git submodule add /src/somegitrepo sub_lvl1
    Cloning into 'sub_lvl1'...
    done.
    % cd sub_lvl1
    % git annex init
    init  (merging origin/git-annex into git-annex...)
    (recording state in git...)
    ok
    (recording state in git...)
    % git submodule add /src/somegitrepo sub_lvl2
    Cloning into 'sub_lvl2'...
    done.
    fatal: Could not chdir to '../../../sub_lvl2': No such file or directory
    Unable to checkout submodule 'sub_lvl2'

### What version of git-annex are you using? On what operating system?
    % apt-cache policy git-annex-standalone
    git-annex-standalone:
      Installed: 6.20160213+gitg9597a21-1~ndall+1

Debian stretch, git-annex from NeuroDebian.

### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)

Yes, lots! Using it for some of its original use cases for more than five years now -- I was actually surprised to learn, just now, that the oldest commit in my music repository is exactly 5 years and 6 days old. Thanks for longevity and reliability!

More recently I aim exploring the use of git annex for managing datasets and their dependencies, i.e. going from raw to some processed state over multiple levels, where each level is a useful starting point for some analysis, and each previous level is a dependency (input) to the next. With just one level above "raw" this has massively improved collaboration workflows in student/teacher settings for me. Deeper nesting levels would allow for even more interesting applications, but see above ;-) I think Git seems needlessly confused, but I don't fully grasp what is happening yet. I'd appreciate any insight you may have. Although it is Git that shows the undesired behavior, it seems it is git-annex that ultimately confused it. Hence I came here first.

BTW: What a nice idea to ask for something like this in a bug report.


[[!meta author=mih]]

> I've verified this is fixed on git's side. With git 2.23.0, my simple
> reproduction script that uses only git does not fail as it used to.
> And, yoh previously followed up that it was fixed in actual git-annex
> use.
> So, [[done]] --[[Joey]]