After a series of pretty convoluted copying files around between annex'd repos and pulling changes around between repos. I noticed that occassionally when git-annex tries to stage files (the `.git-annex/*/*/*logs`) git some times gets wedged and doing a "git commit -a" doesn't seem to work or files might not get added thus leaving a bunch of untracked files or modified files that aren't staged for a commit.

I tried running a *`git rm --cached -f -r *`* then *git add -u .git-annex/* or the usual *git add* then a commit fixes things for me. If I don't do that then my subsequent merges/pulls will fail and result in *no known copies of files* I suspect git-annex might have just touched some file modes and git picked up the changes but got confused since there was no content change. It might also just be a git on OSX thing and it doesn't affect linux/bsd users.

For now it's just a bit of extra work for me when it does occur but it does not seem to occur often.

> What do you mean when you say that git "got wedged"? It hung somehow?
>
> If git-annex runs concurrently with another git command that locks
> the repository, its git add of log files can fail.
> 
> Update: Also, of course, if you are running a "got annex get" or
> similar, and ctrl-c it after it has gotten some files, it can
> end up with unstaged or in some cases un-added log files that git-annex
> wrote -- since git-annex only stages log files in git on shutdown, and
> ctrl-c bypasses that.
> --[[Joey]] 

>> It "got wedged" as in git doesn't let me commit anything, even though it tells me that there is stuff to be committed in the staging area.

>>> I've never seen git refuse to commit staged files. There would have to
>>> be some error message? --[[Joey]] 

>>>> there were no error messages at all

>>>>> Can I see a transcript? I'm having difficulty getting my head around
>>>>> what git is doing. Sounds like the files could just not be `git
>>>>> added` yet, but I get the impression from other things that you say
>>>>> that it's not so simple. --[[Joey]] 

This turns out to be a bug in git, and I have posted a bug report on the mailing list.
The git-annex behavior that causes this situation is being handled as
another bug, [[git-annex directory hashing problems on osx]].
So, closing this bug report. [[done]] --[[Joey]]