How do I install IonCube with a custom php.ini file?

If you create a custom php.ini file, you lose access to ioncube. Litecommerce and x-cart both come with ioncube; so here's how to link it back into your configuration using your custom php.ini

After adding whatever custom PHP settings you need, add the following line to your ini file. You will need to adjust the line to your server settings. Copy and paste the line, then specify the correct path, using your actual cpanel username, and the correct server operating system and OS version.

zend_extension = /home/cpanel_name/public_html/ioncube/ioncube_loader_lin_x.x.so

For threaded php, (most servers with Hands-on are NOT THREADED) the line would look like this:
zend_extension_ts = /home/cpanel_name/public_html/ioncube/ioncube_loader_lin_x.x_ts.so

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