fix(orchestrator): refresh control_refs on PLC re-scans

run_plc_scan's persist block was insert-only, so a PLC re-scan never
updated control_refs on findings first seen before the semantic mapping
pass ran (or before it was enabled) — mappings could only be picked up by
deleting and re-adding the target. Port the refresh branch run_pipeline
already has (#228): when a finding already exists and now carries
control_refs, $set them onto the existing row.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

compliance-agent/src/pipeline/orchestrator.rs

@@ -586,7 +586,21 @@ impl PipelineOrchestrator {
             let Some(path) = ingest_set.get(&a.id).and_then(|ia| ia.working_path.clone()) else {
                 continue;
             };
-            all_findings.extend(crate::pipeline::plc::analyze_tree(&path, target_id));
+            let mut source_findings = crate::pipeline::plc::analyze_tree(&path, target_id);
+            // Control mapping for the PLC path (run_plc_scan is separate from
+            // run_pipeline, which does its own mapping). PLC findings carry
+            // file_path/line/cwe, so the semantic pass reads each region under this
+            // source's `path` and stamps master-control refs. The LUT + grounded
+            // surface passes are code-pattern / CRA-specific and don't apply to
+            // IEC 61131-3 control logic, so only the semantic pass runs here.
+            crate::controls::semantic_stamp_findings(
+                &self.config,
+                self.llm.clone(),
+                &path,
+                &mut source_findings,
+            )
+            .await;
+            all_findings.extend(source_findings);
             // Control-application SBOM: CODESYS libraries + runtime from a
             // `.projectarchive` (uploaded, or committed in the working tree).
             let archive = a
@@ -611,6 +625,7 @@ impl PipelineOrchestrator {
         );
 
         let mut new_count = 0u32;
+        let mut refreshed_count = 0u32;
         for mut finding in all_findings {
             finding.scan_run_id = Some(scan_run_id.to_string());
             if self
@@ -622,8 +637,27 @@ impl PipelineOrchestrator {
             {
                 self.db.findings().insert_one(&finding).await?;
                 new_count += 1;
+            } else if !finding.control_refs.is_empty() {
+                // Re-scan refresh: mirror run_pipeline — persist newly-computed
+                // control_refs onto a PLC finding first seen before the semantic
+                // pass ran. The insert path alone never would, so without this a
+                // PLC re-scan can only pick up mappings via a delete + re-add.
+                self.db
+                    .findings()
+                    .update_one(
+                        doc! { "fingerprint": &finding.fingerprint },
+                        doc! { "$set": { "control_refs": finding.control_refs.clone() } },
+                    )
+                    .await?;
+                refreshed_count += 1;
             }
         }
+        if refreshed_count > 0 {
+            tracing::info!(
+                target_id,
+                "Refreshed control_refs on {refreshed_count} existing PLC findings"
+            );
+        }
 
         if !all_sbom.is_empty() {
             if let Err(e) = self