@stable nymph - Yes. Unless you have some serious reason for doing that refactor, it's far from best practice with Nest. Those three "packages" as the author notes, Domain, Infrastructure and Usecase are usually split in Nest by having a module called "common" or "core" for infrastructure and then all other modules hold both domains and usecases to build a feature. Usecases are called services in Nest. The "domain" is the module. So, in his example, you'd have a "common" folder and a "todo" folder. In the "todo" folder, you'd have controllers, services, interfaces, guards, etc. folders. A mini-onion. Nest puts your modules together to form the big onion.
For a small "todo" application, that might seem strange, but if you have an application with a lot of features, each feature will be its own module and so finding "domain code" and understanding what the application will do is fairly easy. I mean, imagine you have an issue with config in that setup. Where do you go? Domain or Infrastructure? With a proper Nest setup, you'd go to "common/config" and all code will be there in the one (sub-)module.
Or imagine, you'd like to reuse his todo "feature" in some other application aside from a number of other features that application might have. It would be impossible.
His guidance completely breaks Nest's modularisation facility basically denying code reusability for anyone following his advice.