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+It would be nice if I could configure a git repository to be guarded against git-annex. Or even a global git config option to default to not use git-annex but only in specific repositories meant to be used with git-annex.
+
+We've had a source code repository added with git-annex branches (repeatedly) and the user had problems with unwanted git-annex hooks installed in his checkout. I suspect that this was a user error, i.e. running git-annex in the wrong directory, but I would like to put guards into place by disabling git-annex by default and only allowing it for certain specific repos.