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The source code for Drupal is stored in /var/src/drupal. Every domain hosted has to have a symlink to it in /var/www/<domain> (since Apache assumes the DocumentRoot is there).

Multiple sites

All configuration (including uploaded files and possibly modules/themes that are only installed for one site) is located in sites/<domain>/. Modules available to all sites are available in sites/all/. The latter is also the default location where drush installes modules and themes.

Domain aliases: If you want to make the same site available under two domains (e.g. like currently jabber.at, jabber.zone etc. are all the very same Drupal configuration), use sites/sites.php. Note that this is not necessary for "www."-style subdomains.

Drush cheatsheet

Update Drupal core, contrib projects and update database

drush up

Run command for specific site

To e.g. run updatedb for jabber.at:

drush -l jabber.at updatedb