Personally, I recommend that people starting out learning servlets put their
IDE aside until they are comfortable writing, compiling, and deploying at least a simple 'Hello, World' program in a spec compliant container like Tomcat.
I don't know how Netbeans is deploying your apps within Tomcat so I can't be of much help to you.
I'm going to move this
thread to our IDEs forum where you stand a better chance of finding someone who knows what it does.