Don't apply patches or mark patches applied with bin/storage upgrade --dryrun
Summary: Fixes T12682.
Test Plan: Ran bin/storage upgrade --dryrun repeatedly with un-applied patches, saw it not apply them and not mark them applied.
Reviewers: chad
Reviewed By: chad
Maniphest Tasks: T12682
Differential Revision: https://secure.phabricator.com/D17837