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This is noticeable when the upgrade fails, because the symlink isn't restored properly. WHen the upgrade succeeds, the sites go down for the duration of the upgrade but go back up at then end.
Still, we shouldn't destroy that symlink... This is similar to #2118857: upgrading from 1.x ditches a /var/aegir symlink.
Comments
Comment #1
ergonlogicDuplicates #2115129: Symlink to aegir.conf sometimes lost on .deb upgrades