Create sites/all/ subdirs on Aegir Master Instance install and upgrade early enough to avoid warnings on Verify.
Make sure there are no ghost or disabled vhosts which still listen on IP.

Caveats: If you have old enough BOA system which still uses legacy IP mode and not a wildcard in the Nginx 'listen' directive, which is both Aegir and BOA standard for a long time already, this commit will fix the problem and update directives only in vhosts known and controlled by BOA. If you have any other vhosts, located in standard or non-standard Nginx/BOA directories for vhosts, including vhosts to support SSL enabled sites, you have have to update them manually after upgrade to BOA-2.3.0 or newer, or they may take over all other vhosts on the system and cause redirects to /install.php which results with Nginx error 403 or 404, depending on the prior configuration. It will happen because IP based 'listen' directive in Nginx has higher priority, and will mess things horribly if there are vhosts using wildcard and some using IP address.