sounds good.
And the reason for keeping with zone's structure of config_example.json and website_example is when you do a git pull it pulls the new files. If you don't do this then the files wont download and need to be merged prior since they have been changed.
The source files in /lib might have dependencies on new /config.json & /website. That is why you should not pull just a part of the source code but rather merge the full repository instead.