Fix git-fsck errors in the git-bare cooker

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Migrated from T3551 (view on Phabricator)

assigned to @vlorentz

marked this issue as related to swh/meta#3504

added Vault priority:Normal labels

marked this issue as related to swh-storage#3552 (closed)

marked this issue as related to #3553 (closed)

added state:wip label

changed milestone to %Make the git-bare cooker publicly available

added activity::Epic label