Just create a web application project in Netbeans for your final project.

This will allow you to create war files/etc.

You'll need to adjust the war file to work outside netbeans' Tomcat.

Just add the following to the build.xml:

<target name="-post-dist">
   <mkdir dir="${dist.dir}/deploy/tmp"/>
   <unjar src="${dist.war}" dest="${dist.dir}/deploy/tmp"/>
   <delete file="${dist.dir}/deploy/tmp/META-INF/context.xml"/>
   <copy file="${web.docbase.dir}/META-INF/context.xml" todir="${dist.dir}/deploy/tmp/META-INF"/>
   <jar basedir="${dist.dir}/deploy/tmp" destfile="${dist.dir}/deploy/${war.name}" includes="**"/>
   <delete dir="${dist.dir}/deploy/tmp"/>
</target>

This creates the same war file in a 'deploy' sub-directory which can be used outside of netbeans.