Such as CCSpriteFrameCache, CCDictionary::createWithContentsOfFileThreadSafe, CCBMFontConfiguration.
I have to modify cocos2dx source code, When I write self resource pack.
In this case, I would modify CCFileUtils to read from your resource pack, instead of trying to modify all of those other classes.
My resource system is more complex. It has resource pack which is read only and cache pack which is writable. And each file can compress or encode or both separately. By the way, CCFileUtils is os related. So, I need memory interfaces to cache cocos2d-x resource.