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Well when I do this, whats with the conf.d file?
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The apps vhost has already a complete configuration, so you dont need the conf.d file for apps that are installed there. The only thing that needs to be configured is an alias and as I posted above, I will see how this can be integrated in the apps installer.
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BTW Whats with update, delete function for the ispapp?
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The setup.sh script is executed for installation and update. A uninstall function is not available yet.