[[!comment format=mdwn
 username="benjamin.poldrack@d09ccff6d42dd20277610b59867cf7462927b8e3"
 nickname="benjamin.poldrack"
 avatar="http://cdn.libravatar.org/avatar/5c1a901caa7c2cfeeb7e17e786c5230d"
 subject="@joey: Sorry ..."
 date="2017-09-14T12:00:09Z"
 content="""
... I somehow managed to miss your response. Now, since a somewhat related topic is emerging again with datalad, I looked into this one again.
I reproduced, what I described before, but I noticed that it involves kind of an implicit upgrade from a V5 to V6 repository.

First, let's have v5 repo with a file in git and a file in annex:


    ben@tree /tmp % mkdir origin
    ben@tree /tmp % cd origin
    ben@tree /tmp/origin % git init
    Initialized empty Git repository in /tmp/origin/.git/
    ben@tree /tmp/origin % git annex init
    init  ok
    (recording state in git...)
    ben@tree /tmp/origin % echo some > some
    ben@tree /tmp/origin % git add some
    ben@tree /tmp/origin % echo something different > annex
    ben@tree /tmp/origin % git annex add annex
    add annex ok
    (recording state in git...)
    ben@tree /tmp/origin % git commit -m \"initial\"
    [master (root-commit) 8b96354] initial
     2 files changed, 2 insertions(+)
     create mode 120000 annex
     create mode 100644 some
    ben@tree /tmp/origin % ll
    total 376
    drwxr-xr-x  3 ben  ben    4096 Sep 14 13:34 .
    drwxrwxrwt 24 root root 364544 Sep 14 13:33 ..
    lrwxrwxrwx  1 ben  ben     180 Sep 14 13:34 annex -> .git/annex/objects/g7/4P/SHA256E-s20--b6105173f468fc7afa866aa469220cd56e5200db590be89922239a38631379c9/SHA256E-s20--b6105173f468fc7afa866aa469220cd56e5200db590be89922239a38631379c9
    drwxr-xr-x  9 ben  ben    4096 Sep 14 13:34 .git
    -rw-r--r--  1 ben  ben       5 Sep 14 13:34 some
    ben@tree /tmp/origin % git ls-files
    annex
    some
    ben@tree /tmp/origin % git annex find
    annex

Now, clone this repository:

    ben@tree /tmp/origin % cd ..
    ben@tree /tmp % git clone origin cloned
    Cloning into 'cloned'...
    done.
    ben@tree /tmp % cd cloned

And annex-init as a v6 repository:

    ben@tree /tmp/cloned % git annex init --version=6
    init  (merging origin/git-annex into git-annex...)
    (recording state in git...)
    (scanning for unlocked files...)
    ok
    (recording state in git...)
    ben@tree /tmp/cloned % git status
    On branch master
    Your branch is up-to-date with 'origin/master'.

    Changes not staged for commit:
      (use \"git add <file>...\" to update what will be committed)
      (use \"git checkout -- <file>...\" to discard changes in working directory)

    	    modified:   some

    no changes added to commit (use \"git add\" and/or \"git commit -a\")


This kind of \"implicit\" upgrade might not be a common use case, but the result seems to be a bit weird nonetheless.

"""]]