Generally, MVC frameeworks have a structure that looks something like:
/models
/views
/controllers
/utils
However, in a web application sui
I usually group code by feature, so in your case grouping by application would make the most sense to me. The reason is that if I want to work on a particular feature, I shouldn't have to search through three separate folders looking for the components I need. If you group by the high level feature you know everything you need is together.