Well, the directory structure is something similar to this..
|->your application folder ****
|-> All your html and jsp files go here.
|->WEB-INF (This folderwill contain web.xml file)
|->all your compiled java files go here
**** You can name it anything you like. This will the name with which you will invoke the application through browser. Suppose you name it library, you can access it using the browser with the following url
In case you are running it on local machine
Check out the following link too