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System.exit() kills Burp

I'm building an extension that will call a Java command line program from within Burp (by calling the main() method). Unfortunately, when the command line tool finishes, it calls System.exit(0); which doesn't just kill the CLI, it also kills Burp entirely. Is there a way to prevent this in Burp? As a side question, when extensions are submitted to the BApp Store do you check for things like malicious calls to System.exit()?

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