[Bug] Claude Desktop native messaging host intercepts Chrome extension connection, blocking Claude Code integration

Description

When both Claude Desktop app and Claude Code are installed on macOS, the Chrome extension fails to connect to Claude Code with the error: "Browser extension is not connected."

Root Cause

Both Claude Desktop and Claude Code register native messaging host configurations in ~/Library/Application Support/Google/Chrome/NativeMessagingHosts/ with the same allowed_origins extension IDs. The Claude Desktop config (com.anthropic.claude_browser_extension.json) takes precedence, causing the Chrome extension to connect to Claude Desktop's native host instead of Claude Code's.

Environment

• OS: macOS (Darwin 25.2.0)
• Claude Code Version: 2.1.17
• Chrome Extension ID: fcoeoabgfenejglbffodgkkbkcdhcgfn

Steps to Reproduce

1. Have both Claude Desktop app and Claude Code installed
2. Install the Claude Chrome extension
3. Run claude --chrome
4. Try to use any Chrome integration tool
5. Error: "Browser extension is not connected"

Workaround

Replace the Claude Desktop native host config to point to Claude Code:

# Backup the Claude Desktop config
mv ~/Library/Application\ Support/Google/Chrome/NativeMessagingHosts/com.anthropic.claude_browser_extension.json \
   ~/Library/Application\ Support/Google/Chrome/NativeMessagingHosts/com.anthropic.claude_browser_extension.json.backup

# Create new config pointing to Claude Code
cat > ~/Library/Application\ Support/Google/Chrome/NativeMessagingHosts/com.anthropic.claude_browser_extension.json << 'EOF'
{
  "name": "com.anthropic.claude_browser_extension",
  "description": "Claude Browser Extension Native Host",
  "path": "/Users/USERNAME/.claude/chrome/chrome-native-host",
  "type": "stdio",
  "allowed_origins": [
    "chrome-extension://dihbgbndebgnbjfmelmegjepbnkhlgni/",
    "chrome-extension://fcoeoabgfenejglbffodgkkbkcdhcgfn/",
    "chrome-extension://dngcpimnedloihjnnfngkgjoidhnaolf/"
  ]
}
EOF

# Restart Chrome

Expected Behavior

Claude Code and Claude Desktop should be able to coexist without conflicting native messaging host registrations. Possible solutions:

• Use different native messaging host names for each application
• Add a mechanism to switch between Claude Desktop and Claude Code connections
• Detect the conflict and provide a clear error message with resolution steps

Additional Context

The /chrome reconnect option opens Chrome briefly then closes without properly installing the native messaging host when this conflict exists.