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Make test_directory_bogus_perms/test_revision_bogus_perms/ actually test the…

Description

Make test_directory_bogus_perms/test_revision_bogus_perms/ actually test the cookers

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.