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Don't apply patches or mark patches applied with `bin/storage upgrade --dryrun`

Description

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