fix: run dialog logging and reduce tree flash

Co-authored-by: matt-pharr <25289941+matt-pharr@users.noreply.github.com>

Author: Copilot

electron/renderer/src/app/index.tsx

@@ -215,14 +215,29 @@ const App: React.FC = () => {
     setScriptDialog(null);
 
     try {
+      const logEntry: LogEntry = {
+        id:
+          typeof crypto !== 'undefined' && 'randomUUID' in crypto
+            ? crypto.randomUUID()
+            : `log-${Date.now()}-${Math.random().toString(36).slice(2, 6)}`,
+        timestamp: Date.now(),
+        code: `tree.run_script("${scriptDialog.scriptPath}", **params)`,
+      };
+
       const result = await window.pdv.script.run(currentKernelId, {
         scriptPath: scriptDialog.scriptPath,
         params,
       });
 
       if (!result.success) {
         setLastError(result.error);
+        logEntry.error = result.error;
+      } else {
+        logEntry.result = result.result;
+        logEntry.duration = result.duration;
       }
+      setLogs((prev) => [...prev, logEntry]);
+      setNamespaceRefreshToken((prev) => prev + 1);
     } catch (error) {
       const message = error instanceof Error ? error.message : String(error);
       setLastError(message);

electron/renderer/src/components/Tree/index.tsx

@@ -24,7 +24,7 @@ export const Tree: React.FC<TreeProps> = ({ kernelId, refreshToken = 0, onAction
   const expandedPathsRef = useRef<Set<string>>(new Set());
 
   const loadRoot = async (force?: boolean) => {
-    setLoading(true);
+    setLoading(nodes.length === 0);
     setError(undefined);
     if (!kernelId) {
       setNodes([]);