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As I understand it, a Java process running in Console is a special org.eclipse.debug.internal.core.RuntimeProcess that wraps a java.lang.Process. Terminating the RuntimeProcess calls java.lang.Process.destroy(). Unfortunately, Process.destroy() does not run the shutdownhandlers on Windows due to Java Bug Id 4485742. And more unfortunately, this bug is closed. Perhaps you can convince Sun to reopen it. Spending java.lang.Process an additional exit () method (proposed in jerhewet's comment on the bug) seems to be a good idea.
Move to JDT/Debug
*** This bug has been marked as a duplicate of 38016 ***