(I apologize for the hasty writing here; this subject makes me impatient.)
Reading this post from Code Rabbi makes me reflect on project structure and organization. Frankly, most project structures (as from CodeIgniter, Cake, and all the popular frameworks since then) strike me as misdirected. They're examples of why the project maintainers think their code is somehow special and different, and that the application built from it is also somehow special and different.
Your framework and application code are not special. Their code does not go in a special place. There's no need for a top-level "app" directory with its own special subdirectories. There's no need for a special naming convention to keep your different application-specfic code in specific places.
We had PSR-0, and now have PSR-4, and the Composer autoloader, to handle all that for you. Just use namespaces. All you need for code at the top level of your project is a "src" directory, where all your app code goes, just like all your library code goes in a "src" directory in a library package.
Instead of /app/controllers and /app/models, you have /src/Controller and /src/Model, or however else you want to organize your namespaced code. Then there's no need for a special autoloading system or for hard-coded paths just for your application-level code. Add one single line to Composer that points to the src directory and voila, everything inside it loads for you.
That's it. Nothing special. Just like every other library in your system.
(Again, this was hastily written. Please ask for clarfication if you feel you need it.)