feat(cli): migrate console calls to debugLogger and stdioHelpers (M3 Phase 7-9)

Route CLI console.* calls to structured logging:
- Debug/internal diagnostics → debugLogger (logfile)
- User-facing output → writeStdoutLine/writeStderrLine/clearScreen (stdioHelpers)
- Add stdioHelpers.ts with writeStdoutLine, writeStderrLine, clearScreen
- Migrate pre-session files (gemini.tsx, sandbox.ts, config.ts) to stdioHelpers
- Migrate extension/MCP commands to stdioHelpers
- Migrate non-interactive session/control to debugLogger
- Migrate UI hooks and components to debugLogger

packages/cli/src/config/config.ts

@@ -46,6 +46,7 @@ import { mcpCommand } from '../commands/mcp.js';
 
 import { isWorkspaceTrusted } from './trustedFolders.js';
 import { buildWebSearchConfig } from './webSearch.js';
+import { writeStderrLine } from '../utils/stdioHelpers.js';
 
 const VALID_APPROVAL_MODE_VALUES = [
   'plan',
@@ -501,7 +502,7 @@ export async function parseArguments(settings: Settings): Promise<CliArgs> {
         )
         // Ensure validation flows through .fail() for clean UX
         .fail((msg: string, err: Error | undefined, yargs: Argv) => {
-          console.error(msg || err?.message || 'Unknown error');
+          writeStderrLine(msg || err?.message || 'Unknown error');
           yargs.showHelp();
           process.exit(1);
         })
@@ -593,7 +594,7 @@ export async function parseArguments(settings: Settings): Promise<CliArgs> {
 
   // Handle deprecated --experimental-acp flag
   if (result['experimentalAcp']) {
-    console.warn(
+    writeStderrLine(
       '\x1b[33m⚠ Warning: --experimental-acp is deprecated and will be removed in a future release. Please use --acp instead.\x1b[0m',
     );
     // Map experimental-acp to acp if acp is not explicitly set
@@ -727,7 +728,7 @@ export async function loadCliConfig(
     approvalMode !== ApprovalMode.DEFAULT &&
     approvalMode !== ApprovalMode.PLAN
   ) {
-    console.warn(
+    writeStderrLine(
       `Approval mode overridden to "default" because the current folder is not trusted.`,
     );
     approvalMode = ApprovalMode.DEFAULT;
@@ -894,7 +895,7 @@ export async function loadCliConfig(
       sessionData = await sessionService.loadSession(argv.resume);
       if (!sessionData) {
         const message = `No saved session found with ID ${argv.resume}. Run \`qwen --resume\` without an ID to choose from existing sessions.`;
-        console.log(message);
+        writeStderrLine(message);
         process.exit(1);
       }
     }

packages/cli/src/config/settings.ts

@@ -30,6 +30,7 @@ import {
 import { resolveEnvVarsInObject } from '../utils/envVarResolver.js';
 import { customDeepMerge, type MergeableObject } from '../utils/deepMerge.js';
 import { updateSettingsFilePreservingFormat } from '../utils/commentJson.js';
+import { writeStderrLine } from '../utils/stdioHelpers.js';
 
 function getMergeStrategyForPath(path: string[]): MergeStrategy | undefined {
   let current: SettingDefinition | undefined = undefined;
@@ -747,7 +748,7 @@ export function loadSettings(
                   'utf-8',
                 );
               } catch (e) {
-                console.error(
+                writeStderrLine(
                   `Error migrating settings file on disk: ${getErrorMessage(
                     e,
                   )}`,
@@ -769,7 +770,7 @@ export function loadSettings(
                 'utf-8',
               );
             } catch (e) {
-              console.error(
+              writeStderrLine(
                 `Error adding version to settings file: ${getErrorMessage(e)}`,
               );
             }
@@ -907,9 +908,6 @@ export function migrateDeprecatedSettings(
       legacySkills !== undefined &&
       settings.experimental?.skills === undefined
     ) {
-      console.log(
-        `Migrating deprecated tools.experimental.skills setting from ${scope} settings...`,
-      );
       loadedSettings.setValue(scope, 'experimental.skills', legacySkills);
     }
   };
@@ -939,7 +937,8 @@ export function saveSettings(settingsFile: SettingsFile): void {
       settingsToSave as Record<string, unknown>,
     );
   } catch (error) {
-    console.error('Error saving user settings file:', error);
+    writeStderrLine('Error saving user settings file.');
+    writeStderrLine(error instanceof Error ? error.message : String(error));
     throw error;
   }
 }

packages/cli/src/config/trustedFolders.ts

@@ -15,6 +15,7 @@ import {
 } from '@qwen-code/qwen-code-core';
 import type { Settings } from './settings.js';
 import stripJsonComments from 'strip-json-comments';
+import { writeStderrLine } from '../utils/stdioHelpers.js';
 
 export const TRUSTED_FOLDERS_FILENAME = 'trustedFolders.json';
 export const SETTINGS_DIRECTORY_NAME = '.qwen';
@@ -184,7 +185,8 @@ export function saveTrustedFolders(
       { encoding: 'utf-8', mode: 0o600 },
     );
   } catch (error) {
-    console.error('Error saving trusted folders file:', error);
+    writeStderrLine('Error saving trusted folders file.');
+    writeStderrLine(error instanceof Error ? error.message : String(error));
   }
 }