Joel Dice a098926547 run Shutdown.shutdown on exit when using OpenJDK library
The OpenJDK library wants to track and run the shutdown hooks itself
rather than let the VM do it, so we need to tell it when we're
exiting.

Also, in machine.cpp we need to use only the modifiers specified in
the InnerClasses attribute for inner classes rather than OR them with
the flags given at the top level of the class file.
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