MCP Server Not Loading from Project .mcp.json

Bug Report: MCP Server Not Loading from Project .mcp.json

Description

Claude Code is not loading an MCP server that is properly configured in the project's .mcp.json file. The command claude mcp list reports "No MCP servers configured" despite a valid configuration file existing.

Environment

• Platform: Windows (win32)
• Working Directory: C:\Users\geoff\PycharmProjects\photo_dedup
• Project: Git repository

Configuration

The .mcp.json file in the project root contains:

{
  "mcpServers": {
    "serena": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "--from",
        "git+https://github.com/oraios/serena",
        "serena",
        "start-mcp-server",
        "--context",
        "ide-assistant",
        "--project",
        "."
      ],
      "env": {}
    }
  }
}

Steps to Reproduce

1. Create a project-scoped .mcp.json file with the above configuration using claude mcp add --scope project serena -- uvx
2. Run claude mcp list
3. Observe: "No MCP servers configured. Use claude mcp add to add a server."
4. Start Claude Code session
5. Observe: MCP server tools are not available in the session

Expected Behavior

• claude mcp list should show the configured serena server
• Claude Code should load the serena MCP server on startup
• Serena tools (e.g., serena::get_symbol_body, serena::find_referencing_symbols) should be available

Actual Behavior

• claude mcp list reports no servers configured
• MCP server does not load
• No serena tools are available in Claude Code session

Verification

The MCP server command works correctly when run manually:

uvx --from git+https://github.com/oraios/serena serena start-mcp-server --context ide-assistant --project .

Additional Notes

• This configuration was working correctly a couple of hours ago
• Claude Code has been restarted multiple times
• The .mcp.json file has been recreated from scratch with identical results
• The JSON configuration is valid and properly formatted
• No error messages are displayed during Claude Code startup