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/utils/readStdin.ts

@@ -4,6 +4,8 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
+import { writeStderrLine } from './stdioHelpers.js';
+
 export async function readStdin(): Promise<string> {
   const MAX_STDIN_SIZE = 8 * 1024 * 1024; // 8MB
   return new Promise((resolve, reject) => {
@@ -30,7 +32,7 @@ export async function readStdin(): Promise<string> {
         if (totalSize + chunk.length > MAX_STDIN_SIZE) {
           const remainingSize = MAX_STDIN_SIZE - totalSize;
           data += chunk.slice(0, remainingSize);
-          console.warn(
+          writeStderrLine(
             `Warning: stdin input truncated to ${MAX_STDIN_SIZE} bytes.`,
           );
           process.stdin.destroy(); // Stop reading further