Few things are less enjoyable than working on a project where the organization of the application files and modules is garbage, especially if the application is written by people other than you. Keeping your application file tree and module hierarchy clean and tidy will save you and whoever is reading and using your code lots of time in the long run.
Assume that an application you are working on is a generic e-commerce site, with many users who can view and purchase products, leave reviews, and so on.