when running:
    mvn exec:java -Dexec.mainClass=Kshell

with java 9, 10 or 11

with a pom:
<project>
    <modelVersion>4.0.0</modelVersion>
    <groupId>test</groupId>
    <artifactId>test</artifactId>
    <version>1</version>
    <build>
        <sourceDirectory>src</sourceDirectory>
    </build>
    <properties>
        <maven.compiler.source>9</maven.compiler.source>
        <maven.compiler.target>9</maven.compiler.target>
    </properties>
</project>

and source:
public class Kshell {
    public static void main(String[] args) throws Exception {
        jdk.jshell.tool.JavaShellToolBuilder.builder().run(args);
    }
}

maven complains:
jshell> /exit
| Goodbye
[WARNING] thread Thread[Timer-0,5,Kshell] was interrupted but is still
alive after waiting at least 15000msecs
[WARNING] thread Thread[Timer-0,5,Kshell] will linger despite being asked
to die via interruption
[WARNING] thread Thread[Thread-2,5,Kshell] will linger despite being asked
to die via interruption
[WARNING] NOTE: 2 thread(s) did not finish despite being asked to via
interruption. This is not a problem with exec:java, it is a problem with
the running code. Although not serious, it should be remedied.



going through the debugger somewhat it looks like the first is created by
Preferences and calling:
        builder.persistence(new TreeMap());
eliminates this warning (though not if called after the run finishes). the
timer is stored in a static field, and due to the module system i don't
think i can work around this with classloader magic

the second thread appears to be the static field
SourceCodeAnalysisImpl.INDEXER, and again, i don't see any cleanup logic


workaround:
for now i'm calling System.exit(0)