Tomcat's documentation includes a pretty good description of the architecture of a WAR, and WARs are the basis of every
J2EE web application. So it's a good thing to read up on.
Start here:
http://tomcat.apache.org/tomcat-6.0-doc/appdev/index.html
The actual WAR layout information is here:
http://tomcat.apache.org/tomcat-6.0-doc/appdev/deployment.html
There's also a section provided on how to organize project source for building with the
ANT tool. Because of the multitude of different tasks it takes to build a WAR, I recommend you use a command-line build tool like Ant or Maven. Back before they were invented I used scripts and it wasn't much fun.
I make it a firm policy that ALL my projects can be built from the command without an
IDE. While an IDE is a helpful thing to have, you shouldn't have to depend on it to make critical production builds. I learned this the hard way from IDEs that had become incompatible and from projects that people sent me that could only build if I had the exact same brand and version IDE as they did and had configured a lot of desktop-level items the exact same way they had. On top of that, one place I worked did production builds on a non-GUI machine. Where an IDE wouldn't work at all!
The secret of how to be miserable is to constantly expect things are going to happen the way that they are "supposed" to happen.
You can have faith, which carries the understanding that you may be disappointed. Then there's being a willfully-blind idiot, which virtually guarantees it.