The folder structure is well thought as it is.
I'll give you an example on the three you pointed out
models, views & controllers.
Controllers live in the HTTP directory as they deal with requests and responses which are http. It makes sense to have them in there, with other http files such as middleware and responses.
Models yeah, by default they are in the app directory. They're fine there, but if you do start to have a lot of models, a lot of people do move them to a models directory.
Views aren't part of the application code, hence why they're in a resources folder. They're just responsible for displaying data, hence why you'll also see scripts and styles in the resources folder.
Like said above, you can change all of this, but it's not recommended.