A few notes on the extended document root that may be helpful. This is intended to be used when you want to serve JSPs or static content that are located outside of your Websphere App's root. For example, you may have them located under the web root, or anywhere else in the file system. You set the extendedDocumentRoot settings in the ibm-web-ext.xmi file. See an IBM document like:
http://publib.boulder.ibm.com/infocenter/wasinfo/v6r0/index.jsp?topic=/com.ibm.websphere.express.doc/info/exp/ae/rweb_jspengine.html
What they don't tell you is that you cannot accomplish this by changing the ibm-web-ext.xmi file that is created in the WEB-INF directory of the location that you specified when you deployed your app (assuming that you are adding this feature after you have already deployed the app). You have to go to the location where Websphere has created its own deployed copy of the app in the "cell", and change the file there. Note that at this location, you can also make changes to the web.xml file, and you will not have to redeploy the app. For example, the xmi file on my server was located under:
C:\Program Files\IBM\WebSphere\AppServer\profiles\AppSrv01\config\cells\MyServerNode01Cell\applications\MyApp_war.ear\deployments\MyApp_war\MyApp.war\WEB-INF\