Extending with customer specific files

[eluser]pickupman[/eluser]
I would lean in the direction of extending the Loader class. This what is done in the popular HVMC Modular Extensions by wiredesignz. The Loader class looks through a series of folders to try and find what Controller, Library, etc to load.

You would want to extend the code to look into BASEPATH . '/customerX/adaptation' for folders /controllers/, /libraries/, /helpers/, and '/views/' then look into the default location if not found