Recent reports of auto-update not completing. Most likely cause is max_execution_time being set too low. (Default on my box is 30s.)
I think it's fine to set it to unlimited during the one click update. This could be a static function in Piwik:: that we could also call from the archiving code (maybe this is already done?)
In [1407], refs #938 - add Piwik::setMaxExecutionTime()
In [1411], refs #938 - replace set_time_limit() with call to Piwik::setMaxExecutionTime().
In [1408#file3], call Piwik::setMaxExecutionTime(0) for one click update and command line database update.
(For archiving, defer to LaunchArchiving plugin.)