wizardsDone should be saved in database instead of LocalConfiguration File
When handling Projects with multiple instances i think it would be better to store the WizardsDone section in the database instead of saving it in LocalConfiguration.php
99% of migration done in upgradeWizards affects the database and the local state of the application, the LocalConfiguration.php should be consistent over all instances though.
In a common deployment process i would have to process upgrade wizards on the production machine and then pull the changes in LocalConfiguration.php from the production machine.
With the current handling it can happen, that i do the upgrade wizards on a local dev instance and add the LocalConfiguration changes to the repository, when deploying the latest version the production environment "thinks" all wizards have been processed.
I suggest to save the wizards section in sys_registry instead.