Please describe the problem.

git annex init fails on a clone of a sub sub module from a git repo

What steps will reproduce the problem?

This is the archive with sample repo which is used in example below [http://www.onerussian.com/tmp/repl_submodule.tgz]

What version of git-annex are you using? On what operating system?

6.20160307+gitgb095561-1~ndall+1

> tar -xzf repl_submodule.tgz        

> ls -ld datalad_temp_testrepo_Lb8lMD
drwx------ 5 yoh yoh 180 Mar 29 09:06 datalad_temp_testrepo_Lb8lMD/

> git clone datalad_temp_testrepo_Lb8lMD/sub1/sub1
Cloning into 'sub1'...
done.

> cd sub1
INFO.txt  sub1/  sub2/  test-annex.dat@  test.dat

> git annex init
init  fatal: Could not switch to '/sub1/': No such file or directory
ok
(recording state in git...)

> cat .git/config 
[core]
    repositoryformatversion = 0
    filemode = true
    bare = false
    logallrefupdates = true
[remote "origin"]
    url = /tmp/datalad_temp_testrepo_Lb8lMD/sub1/sub1
    fetch = +refs/heads/*:refs/remotes/origin/*
[branch "master"]
    remote = origin
    merge = refs/heads/master
[annex]
    uuid = 7293cd84-98c5-4f8c-b1ff-1c4fadd90ba3
    version = 5

> git annex --debug init 2>&1 | grep -3 "Could not"
[2016-03-29 09:22:21.786669] read: git ["config","--null","--list"]
[2016-03-29 09:22:21.792047] process done ExitSuccess
[2016-03-29 09:22:21.792158] read: git ["--git-dir=../datalad_temp_testrepo_Lb8lMD/sub1/sub1/.git","--work-tree=/sub1/sub1","--literal-pathspecs","show-ref","git-annex"]
fatal: Could not switch to '/sub1/': No such file or directory
[2016-03-29 09:22:21.797597] process done ExitFailure 128
ok
[2016-03-29 09:22:21.800514] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","hash-object","-w","--stdin-paths","--no-filters"]