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Chikigai: It's likely a specific set of circumstances you didn't determine yet.
if there's any variation in stack traces with the exception, posting those would be useful as well.
For example, I didn't even notice this problem (affected were polling and post-commit hook; resolved by adding extra credentials and patching the plugin, respectively) at first, as manually started builds successfully checked out everything, including the external. It's just that no build was able to detect changes in the external location (+ tons of exceptions logged like this one).