I have spring application which uses embedded Jetty instance.
project
| src
| controller
| webapps
| jsp
| WEB-INF
Found this github project : https://github.com/steveliles/jetty-embedded-spring-mvc
This gives a basic startup template project based on maven. It embedded jetty with spring mvc. Good place to start from scratch or to compare and debug what's wrong with current implementation.
The author has done a nice documentation here : http://steveliles.github.io/setting_up_embedded_jetty_8_and_spring_mvc_with_maven.html