Matthew described yet another way on how to do customizations:
"One of the ways that I have done this in the past is to create a "shell" package. i.e. lets say project manager is heavily customized for the client. Then you create the package client-project-manager with www/index.vuh that defaults to converting the url reference to all files in project manager. Then for those files you need customized you can tell that custom packages index.vuh to reference the custom version instead. "
