Looks like Gusty (or something) changes some of the installation for Tomcat 5.5 and it requires some work to get back to normal. Here’s my changes thus far:

sudo rm /usr/share/tomcat5.5/common/endorsed/*
cd /usr/share/tomcat5.5/common/lib
sudo apt-get install libmysql-java
sudo ln -s /usr/share/java/mysql-connector-java.jar

This fist off removes the bad XML jar files that Tomcat is setup with in its endorsed directory. These assume that you only need a subset of JAXP and don’t provide everything (i.e. XSLT). You could also symlink to the rest of the XML jars in /usr/share/java such as xalan2.jar, but I find that the bundled JAXP in the JDK (sun-java6-*) work much better.

The second part symlinks in MySQL drivers into the main installation. This is required if you are going to be setting up JDBC connection pools inside the Tomcat contexts to a MySQL database.

These are it thus far, but if I find more I’ll update this.