[JENKINS-49401] Move Setup Wizard initialization logic to the init reactor. (#3282)

This way, it is guaranteed Jenkins.save() has never been called before
the SetupWizard is executed, and computation of the initial Setup Wizard
state will be correct.

Since the SetupWizard is now executed before reaching the COMPLETED
milestone, a Jenkins.save() call has been added in order to persist any
configuration change done in prior phases.

(cherry picked from commit 9f599911)