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All actions takes about a minute to be applied to the configuration files. You can take a look at the jobqueue if you want to know if a job has been processed already.
IMPORTANT: If you have a character in your mysql root password that the commandline cannot interpret (such as a ! in ours), it will cause update.php to completely wipe! your dbispconfig database. Luckily I made a backup beforehand.
To fix this issue I put single quotes around '-p' and the password on lines 125 and 168 of update.php.
cd /tmp
wget http://www.ispconfig.org/downloads/ISPConfig-3-stable.tar.gz
tar xvfz ISPConfig-3-stable.tar.gz
cd ispconfig3_install/install
php -q update.php
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