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So I try to update using the shell interface as root and and an error appears with the $conf variable.
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The reason for that error message was the failed update before. The ispconfig configuration file was empty so that the shell script could not find the details of the ispconfig system and stopped to ensure that the system is not damaged more. I posted you the link above on how to recover that. A fresh install was not required.
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Then I noticed that the mysql deamon was damaged.
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This was not caused by the ispconfig update, as ispconfig uses mysql, but is does not configure it. If mysql does not start, then you can finf the reason for that eith.er in the syslog file or mysql log file.