F3 SLICE-3: pending-edit registry + sidecar section-merge update (INV-9 groundwork) (#6)

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

src/threadController.ts

@@ -84,7 +84,12 @@ export class ThreadController implements vscode.Disposable {
 
   private persist(state: DocState): void {
     this.selfWrites.add(this.store.sidecarPath(state.docPath));
-    this.store.save(state.docPath, state.artifact);
+    this.store.update(state.docPath, (a) => {
+      a.threads = state.artifact.threads;
+      for (const t of state.artifact.threads) {
+        a.anchors[t.anchorId] = state.artifact.anchors[t.anchorId];
+      }
+    });
   }
 
   private ensureState(document: vscode.TextDocument): DocState {