[[!comment format=mdwn
 username="http://joeyh.name/"
 ip="4.153.2.84"
 subject="comment 3"
 date="2012-09-19T17:32:13Z"
 content="""
I can only guess what this paste operation entails, but as far as I can tell, the error message and the deletion of the file both come from the paste program, not git-annex. 

I know that git-annex assistant will not annex a file while it's still open to be written to. So my hypothesis is that the file is written to, closed, and then the paste program tries to do something else -- perhaps set the mode of the file -- and by that point git-annex has annexed it, and the program deletes the symlink. (So the content is probably buried in the git annex.)

Could you build from git master and in your annex, run:

   git config annex.delayadd 10

That'll add a 10 second grace period for things to finish with files before they get added to the annex.
Perhaps this will be enough to avoid the problem. Feel free to play with the number of seconds..
"""]]