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Jesse: I've seen it too many times when my Jenkins master was still on Windows that I ended up with two partial build dirs. This is how Jenkins deals with it, and my Gradle scripts running on Windows need to do things like if(!f.deleteDir()&&!f.deleteDir()&&!f.deleteDir())throw.... Notably, a similar hack is missing in Job.java for renaming the builds directory, and it tries only once before throwing.
Jakub: Is your Jenkins home on an NFS share?