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Build the cron script so it outputs to a browser and can be run by simply hitting the URL of the script. This is a very common configuration that most major PHP programs support. PHP code can be written to be platform agnostic for the most part.

Yeah, that cPanel topic was us asking their support about this exact issue (Krydos basically runs the place). Using HE's DNS service with a domain to register it here has been reported to work for a few other domains, so it probably works with eu.org as well, but its still an extra step. These noncompliant registrars seem to be growing too, insomuch that it's eventually going to get to a point where we end up having to allow remote domains if we want to keep supporting common providers.

We don't allow exec and shell_exec for security reasons. However, if you have only one or two commands to run, you could use the cron jobs to run that. Please do note that there's a limit of 2 cron jobs per day. If your application requires it for continuous use then I am afraid it wouldn't work.