Please describe the problem.
Due to the very unstable kernel on my laptop atm I need to reboot quite frequently... and this issue with annex assistant immediately starting synchronizing (although I did disable all synchronizations in webapp, so it would be another issue I guess), I wanted just to disable autostart of git-annex altogether. I have removed $HOME/.config/autostart/git-annex.desktop but to my surprise upon gnome crashing/relogin I had the same ssh key passphrase dialog and that file reappeared.
What version of git-annex are you using? On what operating system?
5.20151116+gitg5416a1a-1~ndall+1
closing as it's not been shown how to reproduce this and it seems impossible as described. --Joey
Well, if your system is crashing, the deletion of the file might not be reflected on the disk or something.
It is true that, when git-annex is installed via the standalone tarball, it will try to install the autostart file whenever the assistant is started. But something has to cause the assistant to start, and if you deleted the autostart file, it wasn't that .. so what was it?
/etc/xdg/autostart/git-annex.desktop is part of the git-annex Debian package, but it's a conffile, so if dpkg reinstalls it after it was deleted that would be a dpkg bug. Anyway, it's not a file written by git-annex except during make install with no PREFIX.
I'm going to close this as it's very old and my earlier comment seems valid.