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Edit your project properties for the uPortal project (right click the project root folder and select "properties" from the contextual menu. Select "Java Build Path" from the left hand navigation pane. Click the "Libraries" tab. Select the JRE System Library and click the "Edit..." button. Choose from the alternate JRE pulldown the name of the alternate JRE you created above.
You still need xalan-2-6-0
The Xalan 2.6.0 jar, previously distributed as /lib/xalan.jar, has been renamed to /lib/xalan-2-6-0.jar so as not to collide with the JAXP xalan.jar. You still need to endorse it (the xalan-2-6-0.jar) so that it will override the org.apache.xml APIs in JDK 1.4's rt.jar. You endorse xalan-2-6-0.jar typically by placing it into the /lib/endorsed/ directory of your JRE and the /common/endorsed/ directory of your Tomcat.
What to do if these instructions are insufficient
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