I remember there was something in the upstream Readium Reader code that we tweaked to get things working, too. Should we consider making forks of the relevant repositories so we can document the changes? Or at least keep patches? I think the change to Readium took place before our plugin repository was created. I can't seem to track down our early testing conversation where we found something wrong RE url encoding.
EDIT: whoops! Never mind. I see the included patch for Readium, now. Nothing to see here.