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Make test_directory_bogus_perms/test_revision_bogus_perms actually test the cookers

vlorentz requested to merge generated-differential-D5689-source into generated-differential-D5689-target

Bogus permissions were normalized by git because it was even loaded; so the cooker's normalization was not actually tested.

This commit uses Dulwich instead of git to stage the changes, and monkey-patches Dulwich to prevent it from normalizing.

Migrated from D5689 (view on Phabricator)

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