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Ok, I actually figured some of this out. Here is the method I made that at least appears to work small-scale, but I can't test it full-scale until I figure out my next problem:

public void...

Ok, I'm completely confused about the whole getResource(String) method. I attempted what you did with the getClass().getResource(args[0]); but I got an index out of bounds exception.

Ok, I meant the I want to access files within the Jar that contains the class that is being executed. I am attempting to access some .class files that will be used to create 3 unique Jars. In order...

I'm confused with the JarInputStream class.

JarInputStream takes in an InputStream, but an InputStream of what? Is it the Jar file as an InputStream? It cant be the files inside as an InputStream...