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Configuration warnings are not reliable

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On a configuration check, I have shell_exec to be enabled and a couple of files to be deleted.
My host has disabled PHP-FPM and the shell_exec is now ok, but I don’t think that was the right procedure. Also because it was fine on installation and I wonder why it isn’t now. Any advice?
The files to be deleted are error_log + info.php + matomo-archive-output.log, which also sound like they should not be deleted.
So why is Matomo giving me these wrong warnings?
Thank you

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