This was quite an upgrade, since the original code dated back quite a way. These are some things I need to handle in order to make code more easily applied to an existing project without overwriting customizations:

• Somehow we need to link to a user stylesheet that can override the existing styles. I think the best way to do this is to have a config item in the local_classes.php file (or a config file for just this kind of thing), where you specify the location of a user stylesheet.
• We have a similar problem with the include files, all of which have project-specific data in them, and yet they're in the project repo and will overwrite a project during a checkout. Again, a config file that the user completes is probably the best option.