Taylor is right. I'm currently in the process of restructuring a large L4 app because the directories were a mess.
Once you get over about 10 each of controllers or models, or you start using repositories and services extensively, it makes far more sense to structure an app around components. E.g. Orders, Customers, Transactions and keeping all of the requisite code for each component stored (and namespaced) together.
Otherwise you end up with a polluted root namespace and massive directories with no meaningful organisation.
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