Nearly every php application I work on as a contractor is badly written. The main problem is that developers don't understand the model part of mvc. They put the logic in the controller or overload the DI because they dont know what a design pattern is. The hard part is explaining this to a client who has spent thousands developing a brick
Maybe there is a problem with structuring web apps that way, if a majority of programmers don't understand how to do it.
MVC was invented for graphical user interfaces in the xerox days and dependency injection is handling dependencies in the opposite way that most programming languages are designed.
...and all of this, on a language that was meant to be a template engine.
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