[eluser]ColonelChlorine[/eluser]
Bit of an old thread, but thought I'd throw my 2c in because I ran into the same issue creating my own library which I didn't want CI to interfere with.
I didn't try extending the Common.php file (I don't even think you can because it's just a collection of functions) ... however I wrote my own loader. Threw it in as a helper. It basically accepts a class name, looks for it in the APPPATH."classes" folder and does a require_once().
That's not far off how CI does it's loader, except it does all the singleton + instantiation crap as well.
Works like a charm for me.