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For a change like the FrontController, it sounds that  you might as well be changing the index.php and be very aware of that fact ...

 

If you use mod_rewrite or any other kind of rules, you can already kind of do that, create your own index2.hp or index_custom.php and redirect the rules to that script instead of index.php ... the end result will be that it uses your custom index.php with your defined controller that won't break after an update