I'm searching for a possibility to override build-in function.PECL APD isn't a 
possible solution for me. Is there any other possibility to override a built-in 
function or to disallow the call without manipulation the php.ini?

You can't override existing functions (whether they're built in php ones or ones you make up yourself).

My second problem is that it is needed for a special framework that the 
conenction to a database isn't set global. I need it to ensure that every 
databasecall is through my class.
Is there any possibility for this?

Nope. You can't just disable the function because your class needs to make it, and disable_functions disables that function everywhere, you can't tell it to do it for every file but "x.php".

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