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Is there a way to prevent duplicate content issue with Google by removing index.php from URLs when Full Friendly URLs are enabled?

Cool Deed

By Cool Deed
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Cool Deed Junior Member

Cool Deed

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Hi All,

I hope everyone is well. So I enabled Full Friendly URLs, but Google reports many duplicate content in Search Console.
For eg. https://mydomain.com and https://mydomain.com/index.php have the same content.
https://mydomain.com/login and https://mydomain.com/index.php/login and many others.

My question is, Is there a way to prevent the duplicate content issue with Google by removing index.php from URLs when Full Friendly URLs are enabled?

I must note that I have a hook file that helps make links canonical and is pasted below: 

<?php
if (!defined("WHMCS"))
    die("This file cannot be accessed directly");

add_hook('ClientAreaHeadOutput', 1, function($vars)
{

        $SystemURL = 'https://mydomain.com';
        $url = "https://$_SERVER[HTTP_HOST]$_SERVER[REQUEST_URI]";
        $url = strtok($url, '?');
    return <<<HTML
    <link rel="canonical" href="{$url}"/>
HTML;
});
Thank you.

Kind regards.
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