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[Test] Account for auto-repairing for shard gen file (elastic#112778)
Since elastic#112337, missing shard gen files are automatically reconstructed based on the existing shard snapshot files. If the list of shard snapshot files is complete, it means the repository is effectively not corrupted. This PR updates the test to account for this situation. Resolves: elastic#112769 (cherry picked from commit e1f7814) # Conflicts: # muted-tests.yml
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