refactor: Replace console.error with structured logging and feedback (#12175)

packages/core/src/tools/shell.ts

@@ -9,7 +9,7 @@ import path from 'node:path';
 import os, { EOL } from 'node:os';
 import crypto from 'node:crypto';
 import type { Config } from '../config/config.js';
-import type { AnyToolInvocation } from '../index.js';
+import { debugLogger, type AnyToolInvocation } from '../index.js';
 import { ToolErrorType } from './tool-error.js';
 import type {
   ToolInvocation,
@@ -226,7 +226,7 @@ export class ShellToolInvocation extends BaseToolInvocation<
             .filter(Boolean);
           for (const line of pgrepLines) {
             if (!/^\d+$/.test(line)) {
-              console.error(`pgrep: ${line}`);
+              debugLogger.error(`pgrep: ${line}`);
             }
             const pid = Number(line);
             if (pid !== result.pid) {
@@ -235,7 +235,7 @@ export class ShellToolInvocation extends BaseToolInvocation<
           }
         } else {
           if (!signal.aborted) {
-            console.error('missing pgrep output');
+            debugLogger.error('missing pgrep output');
           }
         }
       }
@@ -424,7 +424,7 @@ export class ShellTool extends BaseDeclarativeTool<
     const commandCheck = isCommandAllowed(params.command, this.config);
     if (!commandCheck.allowed) {
       if (!commandCheck.reason) {
-        console.error(
+        debugLogger.error(
           'Unexpected: isCommandAllowed returned false without a reason',
         );
         return `Command is not allowed: ${params.command}`;