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run_plc_scan is a separate path from run_pipeline and never called the control-mapping passes, so IEC 61131-3 (pump_station.st etc.) findings were persisted with empty control_refs even with mapping enabled. PLC findings carry file_path/line/cwe, so the semantic pass now runs per source (its region is read under that source's working path) and stamps master-control refs. LUT + grounded passes are code-pattern/CRA-specific and don't apply to control logic, so only the semantic pass runs on the PLC path. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>