[BUG] MCP server shows as connected but tools are not registered in session

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 tools are not available to Claude despite claude mcp list showing the server as connected and healthy.

Manually sending tools/list to the server via stdin confirms it responds correctly with 9 tools (create_or_update_file, search_repositories, get_file_contents, etc.). The server is healthy and responding — the tools just aren't being
registered in Claude's tool session.

Environment

• @modelcontextprotocol/server-gitlab v0.5.1
• macOS (Darwin 22.6.0)

What Should Happen?

Tools from a connected MCP server should be discoverable and callable within the conversation.

Error Messages/Logs

Steps to Reproduce

1. Configure an MCP server in ~/.claude.json:

```json
"mcpServers": {
"gitlab": {
"type": "stdio",
"command": "npx",
"args": ["-y", "@modelcontextprotocol/server-gitlab"],
"env": {
"GITLAB_PERSONAL_ACCESS_TOKEN": "...",
"GITLAB_API_URL": "https://my-gitlab-instance.com"
}
}
}

  2. Run claude mcp list — server shows ✓ Connected
  3. In conversation, Claude cannot find any of the server's tools via ToolSearch — all queries return "No matching deferred tools found"

### Claude Model

Opus

### Is this a regression?

I don't know

### Last Working Version

_No response_

### Claude Code Version

2.1.92

### Platform

Anthropic API

### Operating System

macOS

### Terminal/Shell

iTerm2

### Additional Information

_No response_