One of the main changes in Tomcat 5.5 is the loss of the Logger component. Tomcat 5.5 uses Log4J instead, which gives you a much more flexible implementation. The downside is the slightly longer setup.
You also configure default contexts differently. You can configure context information at the server level, the host level and the web application level. Therefore, the <DefaultContext> element of server.xml is no more.
There are a number of changes in the download, where you have to download the Tomcat internal API docs and the admin application separately, though I don't think the admin application is a great loss. I find it temperamental and not very useful.
The manager application has changed slightly and it now has a more uniform deployment mechanism.
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