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Many popular Java Portlets - including several provided by JA-SIG - rely on the ability to share user session data between the portal web application and portlet applications. The JSR-168 specification establishes that this capability shall be provided, but it won't work in Tomcat unless you add the following line to CATALINA_BASE/conf/server.xml:

<!-- A "Connector" represents an endpoint by which requests are received
and responses are returned. Documentation at :
Java HTTP Connector: /docs/config/http.html (blocking & non-blocking)
Java AJP Connector: /docs/config/ajp.html
APR (HTTP/AJP) Connector: /docs/apr.html
Define a non-SSL HTTP/1.1 Connector on port 8080
-->
<Connector port="8080" protocol="HTTP/1.1"
emptySessionPath="true"
connectionTimeout="20000"
redirectPort="8443" />

Example Installations

CalPoly successfully deployed Tomcat 6 with Java 6 with APR, TC-Native, jsvc, jmx.  See the installation and configuration pages from our wiki.