In Jetty 6, if you had
${jetty.home}/contexts/myapp.xml

With Jetty 9.0, move it to
${jetty.home}/webapps/myapp.xml

With Jetty 9.1+, move it to
${jetty.base}/webapps/myapp.xml

Make sure the exploded webapp directory is the same name as your xml file to prevent double deployment.
You also need to change your Context XML File for Jetty 9.
<!DOCTYPE Configure PUBLIC "-//Jetty//Configure//EN" "http://www.eclipse.org/jetty/configure_9_0.dtd"><Configure class="org.eclipse.jetty.webapp.WebAppContext"> <Set name="contextPath">/</Set> <Set name="war"><Property name="jetty.home" default="." />/webapps/myapp</Set></Configure>

Or alternatively, just name your exploded webapp directory
${jetty.home}/webapps/ROOT

Documentation found:
http://www.eclipse.org/jetty/documentation/current/configuring-deployment.html
Updated for Jetty 9.1