So what I did was set up my Tomcat servers virtual host with the file: .../apache-tomcat-6.0.33/conf/Catalina/[sitename]/ROOT.xml:
where [sitename] is the domain name sans "www". I have also set up hosts in server.xml and used the same name there to set an Alias for "www.[sitename]".
<?xml version='1.0' encoding='utf-8'?>
<Context displayName="[sitename]/" path="ROOT" workDir="work/Catalina/[sitename]/_" appBase="home/websites/[sitename]/webapps">
And finally in my webapp/META-INF directory in my project I have context.xml:
<?xml version="1.0" encoding="UTF-8"?>
<Context displayName="[sitename]" path="">
After I have packaged my app as a war I renamed it ROOT.war and put inside the appbase directory where Tomcat picks it up.