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I'd assume that CMS and similar software like wordpress will update their own storage handling, so you'll simply need to get an update for it. They may even use it now, or PDO.
If you've written something custom, and used the mysql library explicitly, than you'll need to rewrite those sections. If you've extended some functionality for something like wordpress, and used their access functions, than the conversion shouldn't need manual changing.
But it's all going to come down to the system's implementation of the mysqli. Since it uses both raw and prepared statements, I don't know what they will do for changes. My *guess* would be that prepared would run through different functionality than the existing ones, and the existing will continue to be raw. This way existing functionality will work without needing to perform modifications to code that currently uses them.
If its in the object oriented world, I'd expect an adapater of some sorts.
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As of PHP 5.5, the MySQL library has been officially deprecated. It is recommended to move to either MySQLi or PDO libraries for your mysql connectivity. See here for help choosing which interface you prefer: http://php.net/manual/en/mysqlinfo.api.choosing.php
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