refactor: streamline debug logging and remove Notifications component

- Remove verbose tool execution debug logs to reduce noise
- Add debug logging for config initialization phases
- Add comprehensive debug logging for skill loading/management
- Add rate limiting for QwenLogger network error logs
- Remove Notifications component from DefaultAppLayout
- Update tests to reflect UI changes and logging behavior

Co-authored-by: Qwen-Coder <qwen-coder@alibabacloud.com>

packages/cli/src/ui/App.test.tsx

@@ -66,7 +66,6 @@ describe('App', () => {
     );
 
     expect(lastFrame()).toContain('MainContent');
-    expect(lastFrame()).toContain('Notifications');
     expect(lastFrame()).toContain('Composer');
   });
 
@@ -98,7 +97,6 @@ describe('App', () => {
     );
 
     expect(lastFrame()).toContain('MainContent');
-    expect(lastFrame()).toContain('Notifications');
     expect(lastFrame()).toContain('DialogManager');
   });
 
@@ -157,6 +155,6 @@ describe('App', () => {
       </UIStateContext.Provider>,
     );
 
-    expect(lastFrame()).toContain('MainContent\nNotifications\nComposer');
+    expect(lastFrame()).toContain('MainContent\nComposer');
   });
 });

packages/cli/src/ui/components/MainContent.tsx

@@ -7,10 +7,12 @@
 import { Box, Static } from 'ink';
 import { HistoryItemDisplay } from './HistoryItemDisplay.js';
 import { ShowMoreLines } from './ShowMoreLines.js';
+import { Notifications } from './Notifications.js';
 import { OverflowProvider } from '../contexts/OverflowContext.js';
 import { useUIState } from '../contexts/UIStateContext.js';
 import { useAppContext } from '../contexts/AppContext.js';
 import { AppHeader } from './AppHeader.js';
+import { DebugModeNotification } from './DebugModeNotification.js';
 
 // Limit Gemini messages to a very high number of lines to mitigate performance
 // issues in the worst case if we somehow get an enormous response from Gemini.
@@ -35,6 +37,8 @@ export const MainContent = () => {
         key={uiState.historyRemountKey}
         items={[
           <AppHeader key="app-header" version={version} />,
+          <DebugModeNotification key="debug-notification" />,
+          <Notifications key="notifications" />,
           ...uiState.history.map((h) => (
             <HistoryItemDisplay
               terminalWidth={terminalWidth}

packages/cli/src/ui/components/Notifications.tsx

@@ -9,7 +9,6 @@ import { useAppContext } from '../contexts/AppContext.js';
 import { useUIState } from '../contexts/UIStateContext.js';
 import { theme } from '../semantic-colors.js';
 import { StreamingState } from '../types.js';
-import { DebugModeNotification } from './DebugModeNotification.js';
 import { UpdateNotification } from './UpdateNotification.js';
 
 export const Notifications = () => {
@@ -23,7 +22,6 @@ export const Notifications = () => {
   return (
     <>
       {updateInfo && <UpdateNotification message={updateInfo.message} />}
-      <DebugModeNotification />
       {showStartupWarnings && (
         <Box
           borderStyle="round"

packages/cli/src/ui/hooks/useGeminiStream.ts

@@ -339,7 +339,7 @@ export const useGeminiStream = (
 
       if (typeof query === 'string') {
         const trimmedQuery = query.trim();
-        onDebugMessage(`User query: '${trimmedQuery}'`);
+        onDebugMessage(`Received user query (${trimmedQuery.length} chars)`);
         await logger?.logMessage(MessageSenderType.USER, trimmedQuery);
 
         // Handle UI-only commands first

packages/cli/src/ui/layouts/DefaultAppLayout.tsx

@@ -6,7 +6,6 @@
 
 import type React from 'react';
 import { Box } from 'ink';
-import { Notifications } from '../components/Notifications.js';
 import { MainContent } from '../components/MainContent.js';
 import { DialogManager } from '../components/DialogManager.js';
 import { Composer } from '../components/Composer.js';
@@ -23,8 +22,6 @@ export const DefaultAppLayout: React.FC = () => {
       <MainContent />
 
       <Box flexDirection="column" ref={uiState.mainControlsRef}>
-        <Notifications />
-
         {uiState.dialogsVisible ? (
           <Box marginX={2} flexDirection="column" width={uiState.mainAreaWidth}>
             <DialogManager