I was debugging through JenkinsRule from Jenkins Test Harness. After the Jetty server and Jenkins have both been terminated in JenkinsRule#after() (line 488 and line 502, respectively) stray threads keep running. Attached is the dump of the running threads. Is it possible to terminate these threads to allow the JVM to exit gracefully?
 
This issue may already have been reported before in this Stack Overflow question: https://stackoverflow.com/questions/13769007/jetty-server-leaves-behind-threads-after-stop
 
A minimal example would be following test code and setting a breakpoint at the System.gc() call on line 517:
 

import org.junit.Rule;
import org.junit.Test;
import org.jvnet.hudson.test.JenkinsRule;

public class RandomTest {
    @Rule
    public JenkinsRule jenkinsRule = new JenkinsRule();

    @Test
    public void randomTest() {
        System.out.println("Hello world");
    }
}

 
I was able to confirm the behaviour with the latest Jetty on both Windows 10 and Linux.
 
This issues was discussed on the developer mailing list: https://groups.google.com/forum/#!topic/jenkinsci-dev/7yL0MKjxQwA