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Fix Directory.from_disk usage

Antoine Lambert requested to merge generated-differential-D2732-source into generated-differential-D2732-target

swh.model.from_disk.Directory.from_disk signature and usage have changed since rDMOD6da524cb2bd8b870eaa0be477837694617cfff1b.

Migrated from D2732 (view on Phabricator)

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