Matt,
Are these the projects you are talking about?
My recommendation would be to simply create a new Angular project using our wizard and copy relevant source from the example projects into this one. The contents of some of the configuration files in your examples may need to be integrated into the existing configuration files (instead of just overwriting the configuration files in the new project). Some key points are noted in the following doc, starting at the “Copy over your app files” section. https://github.com/angular/angular-cli/wiki/stories-moving-into-the-cli#moving-your-project-to-angular-cli
Hope this helps, let us know if you run into any issues.