[Core]: Core framework test gaps (#4) - #18
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…traint matrix Add AuditSpine.from_jsonl for disk verify, extend compare with agent_ref.same and hash_chain_valid, and fill test_core_gaps coverage for config layers, legacy+ULID coexistence, allow/deny/token matrix, session modes, and project storage paths.
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Summary
AuditSpine.from_jsonl()and extendscompare_sessionswithagent_ref.same+hash_chain_valid.Test plan