[eluser]sophistry[/eluser]
I believe that Nummero2 is asking about function name collision rather than filename collision. PHP will cry if you try to load a function that already is loaded. I suppose that is why you ask. One way is to force every function to be wrapped inside the PHP function called function_exists(). see the CI helpers for examples.
Numerro2... have you considered maintaining a "registry" of functions in a db table and checking against when loading functions that so that you don't get the PHP errors on duplicate function declaration? OR maybe just write the errors to the log file and check the log file for any functions that failed the function_exists() check?
I still think you should reconsider your approach... the problems you are posting on these forums are not "normal" problems and probably stem from a
fundamentally flawed initial code architecture decision.