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.
If you copy your jars into the source code directory, they will be in your final jar. Nevetheless, I am not sure if this will work 100% of the time.
There is a great post at java-forum that states the following:
Except for a select few circumstances, what works best for me is to simply merge the files manually. A .jar is basically a .zip with organized contents, and you can open them in almost any .zip capable archive program (I just use gnome's standard archiver, File Roller, and it works great). Backup your jar file and open it in the archiver of your choice, and do the same for each library jar in the library directory. Drag and drop the working folders (IE, everything EXCEPT the META-INF Directory) from each library into your jar's root path (alongside your META-INF and your app's root package). Now drag the META-INF/MANIFEST.MF file from your jar to your Desktop or any other folder. Open it, and erase the Class-Path and X-COMMENT lines. Don't forget to leave a blank newline at the end of the file! Save the new manifest file and drag it back to your jar's META-INF directory, overwriting the old one. Test the jar.