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It's pretty simple, if you throw Spring into the equation. And here it goes:
...
WebAppContext webAppContext = new WebAppContext();
webAppContext.setServer(server);
webAppContext.setContextPath("/");
webAppContext.setResourceBase(new ClassPathResource("webapp").getURI().toString());
server.addHandler(webAppContext);
....
That will make jetty find the necessary web resources inside the jar file.