You can specify a custom webdefault.xml for an individual web application in that webapp’s jetty.xml as follows:

<Configure class="org.eclipse.jetty.webapp.WebAppContext">
  ...
  <!-- Set up the absolute path to the custom webdefault.xml -->
  <Set name="defaultsDescriptor">/my/path/to/webdefault.xml</Set>
  ...
</Configure>

The equivalent in code is:

import org.eclipse.jetty.webapp.WebAppContext;

    ...

    WebAppContext wac = new WebAppContext();
    ...
    //Set up the absolute path to the custom webdefault.xml.
    wac.setDefaultsDescriptor("/my/path/to/webdefault.xml");
    ...

Alternatively, you can use a Jetty Classloading to find the resource representing your custom webdefault.xml.

If you want to apply the same custom webdefault.xml to a number of webapps, provide the path to the file in jetty.xml in the $JETTY_HOME/etc/jetty-deploy.xml file:

   <Set name="defaultsDescriptor"><Property name="jetty.home" default="." />/other/path/to/another/webdefault.xml</Set>

Similarly, when using the Jetty Maven Plugin you provide a customized webdefault.xml file for your webapp as follows:

<project>
    ...
    <plugins>
        <plugin>
            ...
            <artifactId>jetty-maven-plugin</artifactId>
            <configuration>
                <webApp>
                  ...
                  <defaultsDescriptor>/my/path/to/webdefault.xml</defaultsDescriptor>
                </webApp>
            </configuration>
        </plugin>
        ...
    </plugins>
    ...
</project>