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

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