Found a way to perform this enhancement using 0.9-rc-1; but obviously, being able to do so with less code would be nice.

jettyRun.doFirst {
  jettyRun.webAppConfig = new JettyPluginWebAppContext()
  jettyRun.webAppConfig.baseResource = new ResourceCollection(
    [
      "${file(webAppDirName)}", 
      "${rootProject.relativePath(compileGwt.buildDir)}"
    ] as String[])
}

I've found that Richard Bolkey's workaround doesn't work with Gradle 2.5. Specifically the ResourceCollection class isn't available on the build file's classpath. Trying to import the Jetty dependency manually as a build script dependency doesn't solve the issue. I'm guessing that the classloader handling for plugins has changed since 0.9.

As announced on the Gradle blog we are planning to completely migrate issues from JIRA to GitHub.

We intend to prioritize issues that are actionable and impactful while working more closely with the community. Many of our JIRA issues are inactionable or irrelevant. We would like to request your help to ensure we can appropriately prioritize JIRA issues you’ve contributed to.

Please confirm that you still advocate for your JIRA issue before December 10th, 2016 by:

• Checking that your issues contain requisite context, impact, behaviors, and examples as described in our published guidelines.
• Leave a comment on the JIRA issue or open a new GitHub issue confirming that the above is complete.

We look forward to collaborating with you more closely on GitHub. Thank you for your contribution to Gradle!

Thanks again for reporting this issue. We haven't heard back from you after our inquiry from November 15th. We are closing this issue now. Please create an issue on GitHub if you still feel passionate about getting it resolved.