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Can you provide more details that would make this a repeatable bug?
The stack trace shows you are using the command line git implementation. That implementation has no known problems with leaving files open. If you can provide a repeatable case, it has a much better chance of being investigated.
The JGit implementation has known problems with leaving files open (see
JENKINS-19994).There is also a risk that some other program is keeping the files open. There were cases in the past where a virus scanner prevented a directory from being deleted because it was keeping one or more files open from the directory.