skreutzer: Yeah, I know that part is missing in my code, I looked all over the src folder and all I get were .java files, not .class files, last time I coded anything in Java was about 3 years ago so it'll take me time to figure this out, that's why I thought posting here might lure someone more experienced than me.
Since this didn't work I went to a different language, PHP, and it worked for me, I created a website where you can upload an ePub to get it validated much like the online validator
http://validator.idpf.org/ only I provide the options mentioned here:
https://github.com/IDPF/epubcheck/wiki/Running
I originally developed this for my own personal use with my xampp server since the pagina-epubcheck doesn't run on my PC and I really dislike command line. I will of course make this open source (with complete transparency) and hopefully people can give me feedback on upgrades.
You can see what I've done so far in the attached file, If you have any ideas on improvements let me know!
I expect to finish this by tomorrow or two days from now.
Thanks!