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Jesse, where did you see that Util.getDigestOf closes the passed InputStream? I cannot find such a place.
So this issue has probably already been there before https://github.com/jenkinsci/jenkins/commit/9d72311ba0222b9d0489605b8ec2cec711690993
It probably just manifests when fingerprinting a lot of files, since in that case the file descriptor run out, before the GC can discard and close the dangling FileOutputStreams