[BUG] [BashTool] Pre-flight check console.warn corrupts JSON output in Cowork tab, blocking tasks

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Description

When using the Cowork tab in the Claude desktop app, the BashTool pre-flight check warning message corrupts the JSON protocol between the app and the CLI, causing tasks to fail with:

> CLI output was not valid JSON. This may indicate an error during startup. Output: ⚠️ [BashTool] Pre-flight check is taking longer than expected. Run with ANTHROPIC_LOG=debug to check for failed or
slow API requests.

This completely blocks Cowork tab usage. The Chat tab and Code tab work fine.

## Root cause

In cli.js, the pre-flight check has a setTimeout at 10 seconds that calls console.warn(). When Claude Code runs inside the desktop app's Linux VM with gvisor networking, the Haiku API call for
bash command prefix detection takes >10s, triggering the warning. The warning text gets mixed into the JSON output, breaking the desktop app's JSON parser.

## Suggested fix

• Use process.stderr.write() instead of console.warn() and ensure the desktop app doesn't capture stderr as part of the JSON protocol
• Or increase the timeout for VM/cowork contexts
• Or suppress the warning entirely when running in non-interactive/JSON mode

## Environment

• macOS (Darwin 25.2.0, ARM64)
• Claude desktop app (latest)
• Bundled Claude Code VM version: 2.1.34
• System Claude Code: 2.1.39
• coworkNetworkMode: gvisor

What Should Happen?

The Cowork tab should function without errors. The BashTool pre-flight check warning should not be output to stdout/JSON protocol, so it doesn't corrupt the communication between the desktop app and the CLI running in the VM.

Error Messages/Logs

CLI output was not valid JSON. This may indicate an error during startup. Output: ⚠️  [BashTool] Pre-flight check is taking longer than expected. Run with ANTHROPIC_LOG=debug to check for failed or slow API requests.

Steps to Reproduce

1. Open Claude desktop app (latest version, macOS ARM64)
2. Open the Cowork tab
3. Start any task that requires Claude Code to run a bash command
4. Wait ~10 seconds
5. Task fails with: "CLI output was not valid JSON. This may indicate an error during startup. Output: ⚠️ [BashTool] Pre-flight check is taking longer than expected. Run with ANTHROPIC_LOG=debug to

check for failed or slow API requests."

Note: Chat tab and Code tab work fine. Only the Cowork tab is affected.

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

2.1.34

Claude Code Version

2.1.39

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_