You can run setup.sh as many time as you need. It will not hurt your existing installation.

You can either edit setup.sh or just edit the /etc/apache2/sites-enabled/allsky-indi.conf file directly. You just need to restart the apache2 service when finished.

I believe the setup.sh script comments out the Listen directives in ports.conf, so the only file you need to edit is the site.

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