Brian, your project hierarchy should look like this:
+ Project Name
+ src/ <-- Java src files
+ docs/ <-- README's, LICENSE, whatever
+ api/ <-- Generated Javadoc (Project's Javadoc dir)
+ lib/ <-- 3rd party libs you are using to build the src
+ webroot/ <-- Root of your web app, this is the root that gets deployed
+ index.jsp <-- intro page
+ /WEB-INF <-- importnat for web apps
+ lib/ <-- jars needed for your webapp
+ classes/ <-- the build target for your src/ dir above
So when you deploy, “webroot” and everything below it gets copied out to the application server. And when i say “should look like this” I mean “its a good idea to use something like this” but of course structure is really up to the programmer or team.