Do not disable update module in platforms known to include it as required.

This is really silly to include the core "update" module as required and always enabled in any installation profile or feature, yet, some distros like Panopoly and deprecated Martplug does do that for unknown reasons, so disabling this module normally is impossible and forcing disable via Drush disables all other modules chained in the feature, which causes surprises like an empty homepage and other nice results.
Run NewRelic re-install early enough to avoid locking full-upgrade in the waiting forever mode.

This may cause extended downtime during unattended upgrades when there is new version released and the new NewRelic packages may simply hang the process for some weird reason, like probably because of not honoring the non-interactive mode and waiting forever for y/n response. We are avoiding this by uninstalling NewRelic completely before running system full-upgrade and then doing this again if later in the process newer version of PHP happened to be installed.
Fix permissions in the /data/all tree if required.
Re-generate and sync aegir_root password before running Master Instance upgrade.