After upgrading to tomcat 6, the link in server.xml to the default host section no longer lets us link URIs to specific filesystem directories. dynamide manages dynamic paths by mapping them to apps, but also static resources are pushed to a filesystem directory for serving up. This mechanism works for scaling as well, since we could alias Apache to find the files first, use a load balancer, Akami, etc. So there has to be a way to get tomcat to serve up static URIs as well as letting dynamide handle all the rest.
A way to start investigating this would be to get tomcat to serve up /static, which is where the /dynamide/doco app points for javadoc files. The javadoc files are pushed by the "ant javadoc" ant task. Currently, there's an attempt to do the right thing in tomcat's server.xml, though this may not be the right place to do it.