I have inherited a webapp built using NetBean\'s internal ant.
All jsps reside in:
WEB-INF/jsp
And the web.xml has hardcoded links to /
Also note that everything in src/main/resources will be "on the classpath", i.e., it all is copied to my-webapp/WEB-INF/classes when the war is built. So that's a good place to put your configuration files, for example, log4j.xml / logback.xml, or Spring's applicationContext.xml and Spring's other config files, which you can then easily reference with classpath:somefile.xml.
What also makes this very nice is you can set up filters in maven so that it transforms the files from src/resources before it puts them in the war file.
So if you have any config files, other than web.xml, in src/main/webapp/WEB-INF, think about moving them to the src/main/resources directory.