Ok, well naturally I just happen to figure it out as soon as I posted the question.
Here is the code for anyone in the future who has this same issue:
//Where "CreatingJar" is the name of the class this group of code is inside of
JarInputStream in = new JarInputStream(CreatingJar.class.getProtectionDomain().getCodeSource().getLocation().toURI().toURL().openStream());
JarEntry entry = in.getNextJarEntry();
ArrayList<String> entryList = new ArrayList<String>();
entry = in.getNextJarEntry();