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@Nicolas: We just upgraded to 1.480.3, and upgraded these plugin:
As far as I can tell from the plugin docs on <https://wiki.jenkins-ci.org/display/JENKINS/Git+Plugin#GitPlugin-WhyJGit> - it is now using JGit. But the error is still occurring.
Update: Strike the above comment. I had a missing tag in the target repository which caused a very similar error message. Now it works.