[BUG] MCP Server not loading on Windows despite valid configuration

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?

Environment:

• Claude Code Version: 2.1.12
• OS: Windows 11
• Node: [deine version]
• Bun: 1.3.6

Problem:
Custom MCP Server (claude-mem) does not load despite:

• Valid settings.json (both user and project level)
• MCP Server tested manually and works correctly
• Server responds to JSON-RPC initialize requests
• No error messages in any logs

Settings.json:

{
  "mcpServers": {
    "claude-mem": {
      "command": "C:\\Users\\myname\\.bun\\bin\\bun.exe",
      "args": [
        "C:\\Users\\myname\\.claude\\plugins\\marketplaces\\thedotmack\\scripts\\mcp-server.cjs"
      ],
      "env": {
        "CLAUDE_PLUGIN_ROOT": "C:\\Users\\myname\\.claude\\plugins\\marketplaces\\thedotmack"
      }
    }
  }
}

Expected: MCP tools from claude-mem should appear in /tools
Actual: Only built-in tools appear, no claude-mem tools

Manual Test:
Server works when started manually and responds correctly to initialize.

What Should Happen?

Claude Code should load the claude-mem MCP server from settings.json and make its tools (search_memory, get_observations, etc.) available in the tools list.

The MCP server works correctly when tested manually and responds properly to JSON-RPC initialize requests. Settings are valid and configured in both user-level (~/.claude/settings.json) and project-level (.claude/settings.json) locations.

Expected: MCP tools from claude-mem appear when running "What tools do you have available?"
Actual: Only built-in Claude Code tools appear, no claude-mem tools loaded

Error Messages/Logs

Steps to Reproduce

1. Create ~/.claude/settings.json with this content:

{
  "mcpServers": {
    "claude-mem": {
      "command": "C:\\Users\\myname\\.bun\\bin\\bun.exe",
      "args": [
        "C:\\Users\\myname\\.claude\\plugins\\marketplaces\\thedotmack\\scripts\\mcp-server.cjs"
      ],
      "env": {
        "CLAUDE_PLUGIN_ROOT": "C:\\Users\\myname\\.claude\\plugins\\marketplaces\\thedotmack"
      }
    }
  }
}

1. Verify MCP server works manually:

cd C:\Users\myname\.claude\plugins\marketplaces\thedotmack
set CLAUDE_PLUGIN_ROOT=C:\Users\myname\.claude\plugins\marketplaces\thedotmack
bun scripts\mcp-server.cjs
# Server starts and waits for input

1. Start Claude Code:

cd <any-project>
claude

1. Check available tools:

What tools do you have available?

Expected: MCP tools from claude-mem (search_memory, get_observations) should appear

Actual: Only built-in Claude Code tools appear, no claude-mem tools loaded

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.12

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Cursor

Additional Information

_No response_