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I was seeing a lot of sync failure that I first assumed were just associated with #111, but after syncing failed a half dozen consecutive times I looked into it.
www-data@trac:~$ git --git-dir bugs.jqueryui.com/private/repositories/jquery-ui.git/ remote update --prune
Fetching origin
fatal: Unable to create '/var/www/bugs.jqueryui.com/private/repositories/jquery-ui.git/refs/pull/1755/merge.lock': Permission denied
error: Could not fetch origin
I suspect what happened is that I fixed a sync failure as root rather thanwww-data, which resulted in some git internal files having incorrect permissions.
It would be useful if we could detect and log any failures when git.remote('update', '--prune') is called. I didn't see any hints of the failure in the logs, just the downstream error message:
2017-03-03 17:42:33,075 Trac[github] ERROR: Payload contains unknown commit 032ddc3349f625e0840aa8e266b5d8ebee994853