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Fixed in r7534 by having RaiseException use the original Java exception's stack trace. Essentially I just added an instanceof check to RaiseException, so that when it's wrapping a NativeException it does the "more right" thing. Still kinda gross over all since there's multiple levels of wrapping, but removing any of those wrapping layers would be a breaking change we can't really do in 1.1.x.
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I ended up with
output_stream = java.io.ByteArrayOutputStream.new
exception.printStackTrace(java.io.PrintStream.new(output_stream))
LOGGER.fatal(output_stream.to_string)
If I needed the actual stack trace array I would have been SOL.