desktop-commander MCP Tools Not Available in Claude Code Despite Successful Connection

[mimosel]

Environment

• OS: Windows 11
• Claude Code Version: Unknown (logs show appVersion: '0.10.14')
• Node.js Version: v22.15.0
• desktop-commander Version: 0.2.17 (installed globally via npm)
• Installation Method: npm install -g @wonderwhy-er/desktop-commander

Expected Behavior

The desktop-commander MCP server should expose its 25 tools to Claude Code, making them available for use during AI conversations (e.g.,
mcp__desktop-commander__get_config, mcp__desktop-commander__read_file, etc.).

Actual Behavior

• The desktop-commander MCP server successfully connects and reports "Server started and connected successfully"
• The server successfully sends 25 tools to the client (confirmed in logs: "Returning 25 tools (filtered from 25 tools) for client: claude-ai")
• However, none of the desktop-commander tools appear in Claude Code's available tool list
• Attempting to call any desktop-commander tool results in: Error: No such tool available: mcp__desktop-commander__get_config

Comparison with Working MCP Server

For comparison, the sequential-thinking MCP server works correctly:

• Uses identical configuration format (npx with -y flag)
• Tools are available as mcp__sequential-thinking__sequentialthinking ✅
• Can be successfully invoked

Configuration

File: C:\Users\micha\AppData\Roaming\Claude\claude_desktop_config.json

  json
  {
    "mcpServers": {
      "sequential-thinking": {
        "command": "npx",
        "args": [
          "-y",
          "@modelcontextprotocol/server-sequential-thinking"
        ]
      },
      "desktop-commander": {
        "command": "npx",
        "args": [
          "-y",
          "@wonderwhy-er/desktop-commander"
        ]
      }
    }
  }

Steps to Reproduce

1. Install desktop-commander: npm install -g @wonderwhy-er/desktop-commander
2. Add configuration to claude_desktop_config.json (see above)
3. Restart Claude Code completely
4. Wait for MCP servers to initialize (~15 seconds)
5. Attempt to use any desktop-commander tool
6. Observe error: "No such tool available"

Log Evidence

Main Log (connection successful)

2025-10-20 14:26:54 [info] MCP Server connection requested for: desktop-commander
2025-10-20 14:26:54 [info] Launching MCP Server: desktop-commander
2025-10-20 14:26:54 [warn] UtilityProcess Check: Extension desktop-commander not found in installed extensions

desktop-commander Server Log (tools sent successfully)

2025-10-20T12:26:55.919Z [desktop-commander] [info] Message from server:
{"jsonrpc":"2.0","method":"notifications/message","params":{"level":"info","logger":"desktop-commander","data":"Client connected: claude-ai
v0.1.0"}}

2025-10-20T12:26:55.919Z [desktop-commander] [info] Message from server:
{"jsonrpc":"2.0","method":"notifications/message","params":{"level":"info","logger":"desktop-commander","data":"Server connected successfully"}}

2025-10-20T12:26:55.920Z [desktop-commander] [info] Message from server:
{"jsonrpc":"2.0","method":"notifications/message","params":{"level":"debug","logger":"desktop-commander","data":"Returning 25 tools (filtered from
25 total) for client: claude-ai"}}

The log confirms all 25 tools are successfully sent, including:

• get_config
• read_file
• write_file
• execute_command
• start_search
• etc.

Tool Call Attempt

Error: No such tool available: mcp__desktop-commander__get_config

Additional Context

Similar Issues Found

• GitHub Issue #467: "Cannot get any MCP tool calls working at all in Claude Code, despite them working in Claude Desktop"
• GitHub Issue #8407: "MCP Tools Not Available to AI Despite Connected Status"
• GitHub Issue #2682: "MCP Tools Not Available in Conversation Interface Despite Successful Connection"

This suggests a broader Claude Code issue with MCP tool registration, not specific to desktop-commander.

Workaround Attempts

Tried the following without success:

1. ✗ Changed from npx.cmd to npx (matching working sequential-thinking config)
2. ✗ Added -y flag to args
3. ✗ Multiple Claude Code restarts
4. ✗ Verified npm installation path and executable

Questions for Developers

1. Tool Registration: Is there a known issue in Claude Code where MCP servers connect successfully but tools are not registered in the available
   tool catalog?
2. Client Identifier: Logs show client as "claude-ai v0.1.0" - is this correct for Claude Code, or does this indicate the wrong client is
   connecting?
3. Tool Filtering: Could there be a filtering mechanism that's rejecting desktop-commander tools specifically (e.g., tool name validation,
   namespace conflicts)?
4. Debugging: What additional logs or diagnostic information would be helpful to debug this issue?

Impact

This completely blocks the use of desktop-commander functionality in Claude Code, including:

• File system operations
• Terminal command execution
• File search capabilities
• Directory listing
• All 25 tools provided by desktop-commander

Possible Root Cause

Based on investigation, this appears to be a Claude Code tool registration bug rather than a desktop-commander issue, since:

• Server connects successfully ✅
• Tools are sent successfully ✅
• Client receives tool definitions ✅
• But tools never appear in Claude Code's tool catalog ❌