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The stack trace Jesse cites in eb3a4c3 is the following, and this is a very different pattern. This is not from EOF but for Flush, and it wasn't induced by a finalizer. This one smells a genuine reference counting error, and should be tracked separately:
java.lang.NullPointerException at hudson.remoting.ProxyOutputStream$Flush$1.run(ProxyOutputStream.java:305) at hudson.remoting.PipeWriter$1.run(PipeWriter.java:158) at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source) at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at hudson.remoting.SingleLaneExecutorService$1.run(SingleLaneExecutorService.java:111)