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.. and where might I put a new config file please? What should it contain? Sorry I dont understand the way apache2 handles this.. Wouldn't I create contradictory configs if I leave ispconfig's file alone?
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Add a new file in the same directory. Apache reads all files that are in the sites-enabled directory in alphabetical order.
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What I want is to put everything (ISPConfig panel, Webmail (preferred: roundcube) and phpMyAdmin) inside the https- version of the default domain (visible if I use only the IP in the URL, that is)
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The ispconfig panel has aleways its own vhost on a separate port, so it does not run on the default vhost. For a webmail application or phpmyadmin, you use the default vhost.
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I tried, but is says there is no update available so I get no chance to choose ssl, sorry.
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Thats not possible, as the has a version check. I guess you mixed up the ispconfig_update.sh shell script with the update.php file in the ispconfig 3 tar.gz.