The structure of nodejs project is influenced by the personal preferences, project's architecture and module injection strategy being used.Also on event based arc' which uses dynamic module instantiation mechanism. To have a MVC structure it is imperative to separate out the server side and client side source code as the client side code will probably be minimized and sent to browser and is public in its basic nature. And the server side or back-end will provide API to perform CRUD operations
The project above uses browserify and vue.js modules as application base view and minification libs. So the project structure may changes minutely based on which mvc framework you use e.g. The build directory in public will need to contain all the mvc code. You can have a task which does this for you .