[[!comment format=mdwn
 username="yarikoptic"
 avatar="http://cdn.libravatar.org/avatar/f11e9c84cb18d26a1748c33b48c924b4"
 subject="comment 7"
 date="2018-03-23T15:58:15Z"
 content="""
I think it is fixed now, either by git or git-annex . Here is my full protocol to reproduce (needed to adjust paths etc):
[[!format sh \"\"\"
$> mkdir some ; cd some; git init
Initialized empty Git repository in /tmp/some/.git/
1 9949.....................................:Fri 23 Mar 2018 11:55:02 EDT:.
(git)hopa:/tmp/some[master]
$> git submodule add /src/somegitrepo sub_lvl1

fatal: repository '/src/somegitrepo' does not exist
fatal: clone of '/src/somegitrepo' into submodule path '/tmp/some/sub_lvl1' failed
1 9950 ->128.....................................:Fri 23 Mar 2018 11:55:13 EDT:.
(git)hopa:/tmp/some[master]
$> git clone http://datasets.datalad.org/.git /tmp/somegitrepo      
Cloning into '/tmp/somegitrepo'...
1 9951.....................................:Fri 23 Mar 2018 11:55:57 EDT:.
(git)hopa:/tmp/some[master]git
$> git submodule add /tmp/src/somegitrepo sub_lvl1                
fatal: repository '/tmp/src/somegitrepo' does not exist
fatal: clone of '/tmp/src/somegitrepo' into submodule path '/tmp/some/sub_lvl1' failed
1 9952 ->128.....................................:Fri 23 Mar 2018 11:56:12 EDT:.
(git)hopa:/tmp/some[master]git
$> git submodule add /tmp/somegitrepo sub_lvl1    
Cloning into '/tmp/some/sub_lvl1'...
done.
cached/staged changes:                                                                                          
 .gitmodules | 3 +++
 sub_lvl1    | 1 +
1 9953.....................................:Fri 23 Mar 2018 11:56:18 EDT:.
(git)hopa:/tmp/some[master]git
$> cd sub_lvl1 
abide/   adhd200/  crcns/            dbic/   dicoms/  indi/    labs/        nidm/      workshops/
abide2/  corr/     datapackage.json  devel/  hbnssi/  kaggle/  neurovault/  openfmri/
1 9954.....................................:Fri 23 Mar 2018 11:56:24 EDT:.
(git)hopa:/tmp/some/sub_lvl1[master]git
$> git annex init
init  ok
(recording state in git...)
1 9955.....................................:Fri 23 Mar 2018 11:56:27 EDT:.
(git)hopa:/tmp/some/sub_lvl1[master]git
$> git submodule add /tmp/somegitrepo sub_lvl2
Cloning into '/tmp/some/sub_lvl1/sub_lvl2'...
done.
\"\"\"]]
"""]]
