What files to track in version control?

This is probably very basic but not so obvious to me. Every CI app has hundreds of files associated with the project - aside from the files we add such as controllers, views, models, etc. Is there a common strategy for tracking important files using a version control system such as git?

Specifically, do I just need to track my app specific controllers, views and model files, plus maybe the config, routes and assets folders?

Or maybe the whole application folder? 

What strategy do you experienced coders recommend?