Description:
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I can change mysqlnd.net_read_timeout
http://php.net/manual/en/mysqlnd.config.php

via ".user.ini" configuration per-directory file.
And also via ini_set('mysqlnd.net_read_timeout', 10);


I think documentation is incorrect, cause it states 
PHP_INI_SYSTEM (Entry can be set in php.ini or httpd.conf).

There even was a ticket to allow it to be set via ini_set()

https://bugs.php.net/bug.php?id=64952

so just documentation outdated

Test script:
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<?php

$oldTimeout = ini_get('mysqlnd.net_read_timeout');
$newTimeout = rand(1,99);
ini_set('mysqlnd.net_read_timeout', $newTimeout);

echo ($oldTimeout != $newTimeout);