Upgrade preperation removes addons

i ran the following command
curl -s https://mailinabox.email/setup.sh | sudo bash
found here
Mail-in-a-Box Maintenance Guide

once done all my addons for roundcube disappeared.

Is this intended behavior?

Yes, basically you cannot expect any modifications you make to your Mail-in-a-Box installation to survive a run of the setup. This is documented on the installation guide

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