When I run \"clean and build\" the .jar file that is being created only runs if the lib folder is at the same folder of the .jar file.
.jar
lib
You could use Apache Ant since version 1.7 for build the JAR with the required libraries in only one file. You could have a configuration file as follows:
In Netbeans, place the XML file in your project and run it with the context menu.
See more in Apache Ant User Manual.