[BUG] MCP servers connect successfully but tools are not exposed to assistant

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?

MCP servers are connecting successfully and reporting available tools in the debug logs, but these tools never become available to the Claude Code assistant. This issue affects all MCP servers (both user-level and project-level configurations) and persists across complete reinstalls of Claude Code.

What Should Happen?

When an MCP server is configured and connects successfully, its tools should be available to the assistant for use during conversations.

Error Messages/Logs

From ~/.claude/debug/latest:
  2025-11-22T22:42:34.165Z [DEBUG] MCP server "notion": Starting connection with timeout of 30000ms
  2025-11-22T22:42:34.692Z [DEBUG] MCP server "notion": Successfully connected to stdio server in
  529ms
  2025-11-22T22:42:34.693Z [DEBUG] MCP server "notion": Connection established with capabilities:
  {"hasTools":true,"hasPrompts":false,"hasResources":false,"serverVersion":{"name":"Notion
  API","version":"1.0.0"}}

Steps to Reproduce

1. Configure any MCP server (tested with Notion MCP server):

claude mcp add --transport stdio notion --env NOTION_API_KEY=<key> -- /opt/homebrew/bin/npx -y
@notionhq/notion-mcp-server

1. Verify connection: claude mcp list shows "✓ Connected"
2. Start a Claude Code conversation
3. Observe that no mcp__notion__* tools are available to the assistant
4. Check debug logs - they show successful connection

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.0.50

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_