Sometimes, there are things that should be done at the very beginning of execution. And, I called it 'bootstrap' or 'initialization'.
In bootstrap file, I usually disable the magic quotes at the runtime, set up the database adapter,defining paths, registering the autoloader, etc.
Is it right to put that bootstrap in BaseController __construct() method ? Or in the FrontController ?
Or, should I just leave it as bootstrap.php ?
Is bootstrap file a controller?
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No, bootstrap file is for initialization.
A controller is resoponsible for handling user input (requests in a web environment) and providing him an output (responses in a web environment).
A front controller is just a centralized point for handling incomming requests.
None of these compoments should have the responsibility of initializing your application.