Well, it's pretty much done, the development took place on my local xampp server, when I uploaded it to my hosting it didn't work since they block the exec command (i think) by default.
You have to be careful with file upload security.
Anyhow, I am trying to contact them for 2 days now but it seems that all offshore communications for me this holiday is kind of messed up so it will be online soon but i'm not sure when.
In the mean time, like I said, this is totally free and you can download the contents from:
http://odedta.com/projects/epubcheck/epubcheck.zip
Thanks for the GNU thing, I have 0 knowledge on those things ^_^
EDIT: Regarding the usage of jar files in PHP:
In this instance I used the exec command, it's a command I used before in ssh communications when I wanted to server a and stop a server.
You basically write the command line as it is introduced in
https://github.com/IDPF/epubcheck/wiki/Running
PHP Code:
java -jar epubcheck-3.0.1.jar file.epub
Then you just run it using exec()
http://il1.php.net/function.exec
Since the epubcheck-3.0.1 has a built in function to spit out an xml file as the validation log I do that every time a file is checked and using PHP's "simplexml_load_file()" to read the contents then printing them for the user.