[[!comment format=mdwn username="joey" subject="""comment 6""" date="2015-07-02T19:14:40Z" content=""" Yeah, --prune=now is bad news when using git-annex. At least, if you might be doing it at the same time that git-annex is staging objects in the index. Using it in combination with annex.alwayscommit=false is a particularly foot-shootish thing. I've added a warning to its documentation. `git gc` uses a lock file, `.git/gc.pid`. It might be possible for git-annex to hold that lock when it's in the process of staging and committing objects, to avoid `git gc` running at such times. """]]