putting a pak0.pak in your mod's directory will do what i think your asking.
The system works on a higher archy. If something exist on a higher level than the other, the engine uses that instead.
Mod Folders
Pak file in mod directory
Valve Folders
Pak file in Valve directory
There is no need for new code if you replace stuff with the same name in the folder. Names aren't that important, and other things like sprites, sounds, and models can be defined in the mapping part.