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