ionCube24 offers great security in preventing deposited malicious code from being executed. As new files arrive as part of the update process, this will trigger the blocking feature therefore it is advisable to disable WordPress auto-update by adding define( ‘WP_AUTO_UPDATE_CORE’, false ); to the wp-config.php file.
If you have command line access to your site, one solution to allow WordPress updates to function alongside ionCube24 is through use of the wonderful WP-CLI (https://wp-cli.org/) tool. This tool provides a rich interface to WordPress administration from the command line, providing amongst others, features which will upgrade the core, plugins and themes.
A simple curl request to suspect security for the update to the function, within a small shell script, will allow you to automate the process.
First though, ensure that ionCube24 is setup with only the plugins directory or plugins you are specifically interested in are whitelisted for update and/or the core too, should this be desired. Then, the following shell script would update all of WordPress:
#!/bin/sh
curl -sS -d {' "trustpoint_delta": 3 }' \
-X POST -H 'Authorization: API key="XYsdfhooufhukwerhuosrghoisgho348734sdfbukZ"' \
-H 'Content-Type: application/json' https://ioncube24.com/api/v1/domains/xyz.com/trustpoint
wp plugin core update
wp plugin update --all
wp theme update --all
wp core language update
The above WordPress updates can of course be tailored to your own requirements, with the crucial curl request being substituted with your own API key and domain to suspend the security for this process. Further details can be found at https://ioncube24.com/help/faq