I wonder if we shouldn't run every web application for a given build in a single instance as the default. For example, jettyRun and jettyRunWar would simply add the web application to the shared instance (starting it if it is not running). Simimarly, jettyStop would remove the web application from the shared instance (stopping it if there are no web apps left).

In my experience that is preferable. I can see instances where it would be beneficial to be able to run in separate instances though. Consider simulating a network of servers interoperating, perhaps you want some instances to fail and test recovery. So that needs to still be an option.

I am trying to think of cases where this default would be a problem and thus far I am unable to.

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The Jetty plugin has been deprecated and is scheduled to be removed with Gradle 4.0. We are not going to work on this issue anymore.