[BUG] Using native UI in VSCode extension prevents MCP servers from connecting

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?

When using the native UI in the VSCode extension for Claude Code, on startup, MCP servers seem to be unable to connect or are delayed massively. Even if they do connect they'll fail to load properly (tools are undiscoverable, etc.). This is a non-issue when running Claude from terminal, where it is able to connect to the same MCPs nearly instantly and without error.

What Should Happen?

This used to work on the native UI but in some recent update it no longer does. /MCP displays the following and never updates or even shows servers it's trying to connect to until connecting to them some minute(s) later.

<img width="541" height="204" alt="Image" src="https://github.com/user-attachments/assets/84553724-8657-4d06-aa4a-1bf30fb1c0c8" />

Error Messages/Logs

# Error message when attempting to use a tool from a "connected" MCP after a delayed initialization/connection
<tool_use_error>Error: No such tool available: mcp_tool_name</tool_use_error>

Steps to Reproduce

1. Launch Claude Code via VSCode extension using native UI
2. Type /MCP (just to monitor MCP connection status)
3. Wait until it connects to a server, and if it does, attempt to use some tools (fails to find tools)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

Unsure. Was working post-2.x.x update when native UI was introduced.

Claude Code Version

2.0.57 (Claude Code)

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

WSL (Windows Subsystem for Linux)