Persist provider reasoning and assistant text separately on agent_reasoning_audit
(DeepSeekAssistantMessage path), extract diagnosis_run.conclusion, enrich RAG
tool audit (step_id/query/qualityScore), gate empty mysql tools, drop devtools,
and align MVP docs after live E2E verification.
Add repairable INVALID_PROGRESS_PROTOCOL observations, independent
PROGRESS_PROTOCOL_VIOLATED saturation, and controlled release paths.
Archive the OpenSpec change after syncing main specs and devflow.