[BUG] MCP servers configured via CLI don't load in VSCode extension

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?

Bug:

Environment:

• VSCode Extension: 2.1.38
• macOS: Darwin 25.2.0
• MCP servers: figma, atlassian (both HTTP)

Configuration:

• Servers in ~/.claude.json (user scope): ✓
• Servers in .mcp.json (project scope): ✓
• enabledMcpjsonServers set: ✓
• CLI works: ✓ (claude mcp list shows connected)
• VSCode extension: ✗ (/mcp shows nothing, tools not available)

What Should Happen?

mcp connections should reflect in the vs code extension

Error Messages/Logs

Steps to Reproduce

Steps tried:

• Reloaded VSCode window
• Fully quit and restarted VSCode
• Reset project choices
• Added to user scope
• No errors in extension logs

Claude Model

Opus

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

2.1.38

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_