Feel free to put your code wherever you want. Maybe there are some tips for doing it in a diferent way, but mostly the directory tree should be a personal choise and you can put your classes where you feel makes most sense for you. Also you're right with PSR-4, if you make app\MyClasses\Points.php then you could use your code something like new App\MyClasses\Points and will work. Remember to use composer dumpautoload before that.
Personally I sometimes use app\Classes, app\Classes\Interfaces, app\Classes\Abstracts for most basics projects.
Also, you could make a composer package and then a service provider and then a facade and share it with your friends or the comunity.
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