I've been looking for the answer to this for a couple weeks.
Follow these instructions for JBoss:
http://tapomay.blogspot.com/2011/11/clean-urls-with-drupal-urlrewritefilter.html
He links to an article where one had done this for Tomcat: http://www.brianshowalter.com/blog/running_drupal_on_quercus
In a nutshell, you want to rewrite the URL only IF the requested file or directory do not exist on the system. This is why just UrlRewriteFilter is not enough. You have to add a class-filter to UrlRewriteFilter to check for this.
The instructions I linked to uses an older version of UrlRewriteFilter (3.2.0), it probably works just as well with the newer version (I did it with 3.2.0).
You will use that in conjunction with a class filter (there is a google project repository for this, thanks to the author of the linked article, at https://code.google.com/p/drupalrewritefilter/ )
The instructions say to add the files to Eclipse, but I used Netbeans (just start a new project with existing sources).
You'll need to add the servlet.api.jar (some where on your system, if you have J2EE installed) and the UrleRewriteFilter.jar file you are using to the classpath for the build.
Place the resulting drupalrewritefilter.jar
file and the UrlRewriteFilter.jar
file you are using in WEB-INF/lib
Your WEB-INF/web.xml should have this filter directive:
<filter>
<filter-name>UrlRewriteFilter</filter-name>
<filter-class>org.tuckey.web.filters.urlrewrite.UrlRewriteFilter</filter-class>
<init-param>
<param-name>logLevel</param-name>
<param-value>TRACE</param-value>
</init-param>
</filter>
<filter-mapping>
<filter-name>UrlRewriteFilter</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>
Use this instead of the one the website for UrlRewriteFilter says to use.
NOTE: The Quercus install contains a DOCTYPE tag in the beginning for the Servlet API 2.2 or 2.3. But the <filter>
tag is in the Servlet API 2.4 or higher. Your app will error-out unless you either link to a new Server API DTD or (and this is what I did) just delete the DOCTYPE tag all together.
Then you should have a WEB-INF/urlwrite.xml with:
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE urlrewrite PUBLIC "-//tuckey.org//DTD UrlRewrite 4.0//EN"
"http://www.tuckey.org/res/dtds/urlrewrite4.0.dtd">
<urlrewrite>
<class-rule class="com.brianshowalter.drupalrewrite.DrupalRule" />
</urlrewrite>
Reload your drupal app, and then go enable clean URLS's