Seems like a bit of animosity toward Tomcat has finally helped me make progress, mostly because it got all you gurus to actually explain a bit of how it works, and how it's packaged, all concepts I didn't understand. I'm a scientist, not a programmer. I'm new to Ubuntu and Tomcat. My colleagues have been completely unhelpful in this process. It works on their systems, so they've just left me to struggle on my own.
My frustration is further fueled by the fact that the web site that our application will soon handle (http://neuroanalysis.org/toolkit/) is working just fine as static html; it doesn't change much, and most of the pages (not viewable externally) are generated automatically from code, using m2html or doxygen. But now they want me to integrate this site into the JSP format seen at the root (http://neuroanalysis.org/), despite the fact that I have zero experience with Tomcat, Java, or JSP, and nearly no web application development experience. It would have been nice if Tomcat just worked, out of the box, but it took me a couple days just to get it up and running. Now Tomcat works, at least the default page and the example webapps, but the application that my colleagues built won't work. This is their fault, as far as I'm concerned, yet there's nothing I can do to force them to improve what is probably sloppy code on their part. So I'm just looking for some help. Sorry to insult Tomcat, but thanks for the useful feedback. I'll work on the suggestions and let you know if I can't make any progress. :) Michael