[BUG] MCP server tools not available in session despite "✓ Connected" status

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 server shows as "✓ Connected" via claude mcp list, but its tools are NOT available to the model during sessions (not in deferred tools, not discoverable via ToolSearch).

What Should Happen?

MCP server's tools should work

Error Messages/Logs

Steps to Reproduce

1. claude mcp add gitlab --scope user --transport stdio -e GITLAB_PERSONAL_ACCESS_TOKEN="..." -e GITLAB_API_URL="https://my-gitlab.example.com" -- /opt/homebrew/bin/npx -y @modelcontextprotocol/server-gitlab
2. claude mcp list → shows gitlab: ... - ✓ Connected
3. Start a new Claude Code session
4. Ask Claude to use any gitlab MCP tool → tools are not found

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.84

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

## What I tried

• Added server with --scope user, --scope project, and --scope local
• Added config to ~/.claude.json, ~/.claude/settings.json, and .mcp.json
• Verified server starts correctly on stdio and responds to tools/list with valid tools
• Multiple session restarts
• Used full path to npx (/opt/homebrew/bin/npx)
• Confirmed with a test script that the server responds to JSON-RPC tools/list

## Environment

• macOS (Darwin 25.0.0, ARM)
• Claude Code CLI (latest)
• Node.js 25.8.2 (Homebrew)
• MCP server: @modelcontextprotocol/server-gitlab (deprecated but functional)
• Self-hosted GitLab instance