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The leaked files plugin (run on Debian Linux) showed at least one leaked file handle from the RevWalk allocated in the ChangelogCommand of the JGit implementation. I've created a series of changes which were able to fix the condition detected by the leaked files plugin, but still did not allow me to delete the workspace on my Windows machine.
I assume the fixes to the issues detected by the leaked files plugin are a necessary part of the final fix, but they are not sufficient to fix the problem on Windows. Unfortunately, I don't know how to run the leaked files plugin on Windows, it fails to execute there.
If you'd like to see my current prototype (not yet ready for a pull request), refer to https://github.com/MarkEWaite/git-client-plugin/tree/JENKINS-19994-cannot-delete-jgit-workspace