The developer could set a configuration variable to let WebBeans know that they will be taking responsibility for initiating the shutdown sequence when it makes sense for their app, and hence WebBeans needn't do any automatic shutdown sequence. This could be done programatically:

public void (@Observes Deployed Manager manager, @Parameters List<String> params, @Current Configuration config) {
config.setManualShutdown(true);
System.out.println("You provided " + params.size() + " parameters. Well done.");
}

Alternatively this could be done by setting a property in beans.xml or beans.properties.