My guess would be you would modify your bamboo master to use https in your BAMBOO_HOME/bamboo.cfg.xml file..
For the agent, based on the bamboo.cfg.xml, i would assume you might be able to pass 'bamboo.jms.broker.client.url' as another java.additional in the wrapper.conf
or you might be able to set it in the AGENT_HOME/bamboo-agent.cfg.xml, but i can't really find any documentation on it..
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