MCP Server Management

Status: Production Ready Last Updated: 2025-12-06 Dependencies: Node.js 18+, Claude Desktop, winadmin-powershell skill Latest Versions: Claude Desktop 0.7.x, Node.js 22.x

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Quick Start (10 Minutes)

1. Verify Prerequisites

# Check Node.js (required for most MCP servers)
node --version   # Should be 18+

# Check npm
npm --version

# Verify Claude Desktop installed
Test-Path "$env:APPDATA\Claude\claude_desktop_config.json"

2. Locate Config File

# Claude Desktop config location
$configPath = "$env:APPDATA\Claude\claude_desktop_config.json"

# Read current config
Get-Content $configPath | ConvertFrom-Json | ConvertTo-Json -Depth 10

3. Install Your First MCP Server

# Example: Install filesystem MCP server
npm install -g @modelcontextprotocol/server-filesystem

# Add to Claude Desktop config (see Configuration section)

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Critical Rules

Always Do

• Backup claude_desktop_config.json before editing
• Use absolute paths for all executables and arguments
• Restart Claude Desktop after config changes
• Test MCP servers in isolation before adding to config
• Log all MCP installations to your registry

Never Do

• Use relative paths in MCP server configurations
• Edit config while Claude Desktop is running (can corrupt)
• Install MCP servers without verifying Node.js compatibility
• Mix npx and global npm installations for same server
• Forget to escape backslashes in JSON (\\ not \)

---

Claude Desktop Configuration

Config File Location

Windows: %APPDATA%\Claude\claude_desktop_config.json
macOS:   ~/Library/Application Support/Claude/claude_desktop_config.json
Linux:   ~/.config/Claude/claude_desktop_config.json

PowerShell:

$configPath = "$env:APPDATA\Claude\claude_desktop_config.json"

Config File Structure

{
  "mcpServers": {
    "server-name": {
      "command": "node",
      "args": ["path/to/server.js"],
      "env": {
        "ENV_VAR": "value"
      },
      "disabled": false
    }
  }
}

Configuration Fields

Field	Required	Description
command	Yes	Executable to run (node, npx, python, etc.)
args	Yes	Array of arguments passed to command
env	No	Environment variables for the server
disabled	No	Set true to disable without removing

---

MCP Server Installation Patterns

Pattern 1: NPX (Recommended for Quick Setup)

{
  "mcpServers": {
    "filesystem": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-filesystem",
        "C:/Users/Owner/Documents"
      ]
    }
  }
}

Pros: Always uses latest version, no global install needed Cons: Slower startup, requires internet on first run

Pattern 2: Global NPM Install

# Install globally
npm install -g @modelcontextprotocol/server-filesystem

{
  "mcpServers": {
    "filesystem": {
      "command": "node",
      "args": [
        "C:/Users/Owner/AppData/Roaming/npm/node_modules/@modelcontextprotocol/server-filesystem/dist/index.js",
        "C:/Users/Owner/Documents"
      ]
    }
  }
}

Pros: Faster startup, works offline Cons: Manual updates needed

Pattern 3: Local Clone (For Development/Customization)

# Clone to MCP directory
cd D:/mcp
git clone https://github.com/org/mcp-server-name.git
cd mcp-server-name
npm install
npm run build

{
  "mcpServers": {
    "server-name": {
      "command": "node",
      "args": ["D:/mcp/mcp-server-name/dist/index.js"]
    }
  }
}

Pros: Full control, can modify source Cons: Manual updates, more disk space

Pattern 4: Python MCP Server

{
  "mcpServers": {
    "python-server": {
      "command": "python",
      "args": ["-m", "mcp_server_package"],
      "env": {
        "PYTHONPATH": "D:/path/to/server"
      }
    }
  }
}

---

The Three MCP CLI Tools

Windows systems commonly use three MCP servers for CLI operations:

1. Desktop Commander (Primary for Local Work)

Package: @anthropic-ai/desktop-commander Best For: File operations, code editing, persistent sessions

{
  "mcpServers": {
    "desktop-commander": {
      "command": "npx",
      "args": ["-y", "@anthropic-ai/desktop-commander"]
    }
  }
}

Tools Provided:

• read_file - Read file contents
• write_file - Write/create files
• edit_block - Surgical code edits with diff
• list_directory - List directory contents
• search_files - Search for files by pattern
• get_file_info - File metadata
• start_process - Start persistent process
• interact_with_process - Send input to process
• read_process_output - Get process output
• get_config / set_config_value - Configure server

Key Features:

• Persistent process sessions (maintains state)
• Better PATH handling
• Diff-based code editing
• Interactive REPL support

2. Win-CLI (SSH and Multi-Shell)

Best For: SSH operations, remote servers, multiple shell types

{
  "mcpServers": {
    "win-cli": {
      "command": "node",
      "args": [
        "D:/mcp/win-cli-mcp-server/dist/index.js",
        "--config",
        "D:/mcp/win-cli-mcp-server/config.json"
      ]
    }
  }
}

Tools Provided:

• execute_command - Run shell command
• ssh_execute - Run command on remote server
• ssh_connect - Connect to SSH server
• list_ssh_connections - List configured SSH connections

Key Features:

• Multiple shell support (PowerShell, CMD, Git Bash)
• Pre-configured SSH connections
• Isolated shell sessions

Win-CLI Config (config.json):

{
  "shells": {
    "powershell": {
      "enabled": true,
      "command": "C:\\Program Files\\PowerShell\\7\\pwsh.exe",
      "args": ["-Command"]
    },
    "cmd": {
      "enabled": true,
      "command": "cmd.exe",
      "args": ["/c"]
    }
  },
  "ssh": {
    "connections": [
      {
        "id": "server-1",
        "host": "192.168.1.100",
        "username": "admin",
        "privateKeyPath": "C:/Users/Owner/.ssh/id_rsa"
      }
    ]
  },
  "security": {
    "allowedPaths": ["D:/", "C:/Users/Owner"],
    "blockedCommands": ["format", "shutdown", "rm -rf /"],
    "commandTimeout": 60
  }
}

3. Claude Code MCP (Complex Multi-File Tasks)

Package: @anthropic-ai/claude-code-mcp Best For: Complex refactoring, git workflows, multi-file edits

{
  "mcpServers": {
    "claude-code-mcp": {
      "command": "node",
      "args": ["D:/mcp/claude-code-mcp/dist/index.js"],
      "env": {
        "CLAUDE_CLI_PATH": "C:/Users/Owner/AppData/Roaming/npm/claude.cmd"
      }
    }
  }
}

Tools Provided:

• claude_code - Execute Claude Code CLI with prompt

Key Features:

• Wraps official Claude Code CLI
• Auto-bypasses permissions for automation
• Best for complex multi-file operations

When to Use:

// Complex refactoring
claude_code({
  prompt: "Refactor all API calls to use async/await",
  workFolder: "D:/project"
})

// Git workflows
claude_code({
  prompt: "Stage changes, commit with message, push to develop",
  workFolder: "D:/project"
})

Tool Selection Guide

Task	Recommended Tool	Reason
Read/write files	Desktop Commander	Native file tools
Edit code blocks	Desktop Commander	Diff-based editing
Run local commands	Desktop Commander	Better PATH handling
SSH to remote server	Win-CLI	SSH support
Use specific shell	Win-CLI	Multi-shell support
Complex refactoring	Claude Code MCP	Multi-file awareness
Git operations	Claude Code MCP	Git workflow support
Interactive REPL	Desktop Commander	Persistent sessions

---

MCP Installation Workflow

Step-by-Step Process

# 1. Check if server exists in registry (if using registry)
$registry = Get-Content $env:MCP_REGISTRY | ConvertFrom-Json
$registry.mcpServers.'server-name'

# 2. Backup current config
$configPath = "$env:APPDATA\Claude\claude_desktop_config.json"
Copy-Item $configPath "$configPath.backup.$(Get-Date -Format 'yyyyMMdd-HHmmss')"

# 3. Install server (choose method)
# Option A: NPX (no install needed)
# Option B: Global npm
npm install -g @org/mcp-server-name
# Option C: Local clone
cd D:/mcp && git clone https://github.com/org/mcp-server.git

# 4. Read current config
$config = Get-Content $configPath | ConvertFrom-Json

# 5. Add server to config
$config.mcpServers | Add-Member -NotePropertyName "server-name" -NotePropertyValue @{
    command = "node"
    args = @("D:/mcp/mcp-server/dist/index.js")
}

# 6. Save config
$config | ConvertTo-Json -Depth 10 | Set-Content $configPath

# 7. Update registry (if using)
# Add entry to mcp-registry.json

# 8. Log installation
Log-Operation -Status "SUCCESS" -Operation "MCP Install" -Details "Installed server-name" -LogType "installation"

# 9. Restart Claude Desktop
Stop-Process -Name "Claude" -ErrorAction SilentlyContinue
Start-Process "$env:LOCALAPPDATA\Programs\Claude\Claude.exe"

# 10. Test server
# Open Claude Desktop and verify server tools are available

---

MCP Registry Pattern

Maintain a central registry of installed MCP servers:

Registry Schema

{
  "lastUpdated": "2025-12-06T12:00:00Z",
  "mcpServers": {
    "desktop-commander": {
      "installed": true,
      "installDate": "2025-10-01",
      "installMethod": "npx",
      "version": "latest",
      "purpose": "File operations and persistent sessions",
      "configPath": null,
      "notes": "Primary tool for local file operations"
    },
    "win-cli": {
      "installed": true,
      "installDate": "2025-10-01",
      "installMethod": "local-clone",
      "version": "1.0.0",
      "purpose": "SSH and multi-shell support",
      "configPath": "D:/mcp/win-cli-mcp-server/config.json",
      "notes": "Deprecated upstream, using local fork"
    },
    "filesystem": {
      "installed": true,
      "installDate": "2025-10-15",
      "installMethod": "npm-global",
      "version": "0.6.2",
      "purpose": "Filesystem access for specific directories",
      "configPath": null,
      "notes": "Limited to Documents folder"
    }
  }
}

Registry Update Script

function Update-McpRegistry {
    param(
        [string]$ServerName,
        [string]$InstallMethod,
        [string]$Version,
        [string]$Purpose,
        [string]$ConfigPath,
        [string]$Notes
    )

    $registryPath = $env:MCP_REGISTRY
    $registry = Get-Content $registryPath | ConvertFrom-Json

    $entry = @{
        installed = $true
        installDate = (Get-Date -Format "yyyy-MM-dd")
        installMethod = $InstallMethod
        version = $Version
        purpose = $Purpose
        configPath = $ConfigPath
        notes = $Notes
    }

    if ($registry.mcpServers.PSObject.Properties.Name -contains $ServerName) {
        $registry.mcpServers.$ServerName = $entry
    } else {
        $registry.mcpServers | Add-Member -NotePropertyName $ServerName -NotePropertyValue $entry
    }

    $registry.lastUpdated = (Get-Date -Format "yyyy-MM-ddTHH:mm:ssZ")
    $registry | ConvertTo-Json -Depth 10 | Set-Content $registryPath

    Write-Host "Updated registry: $ServerName" -ForegroundColor Green
}

---

Common MCP Servers

Official Anthropic Servers

Server	Package	Purpose
Filesystem	@modelcontextprotocol/server-filesystem	File system access
GitHub	@modelcontextprotocol/server-github	GitHub API integration
GitLab	@modelcontextprotocol/server-gitlab	GitLab API integration
Slack	@modelcontextprotocol/server-slack	Slack integration
Google Drive	@modelcontextprotocol/server-gdrive	Google Drive access
PostgreSQL	@modelcontextprotocol/server-postgres	Database queries
SQLite	@modelcontextprotocol/server-sqlite	SQLite database
Puppeteer	@modelcontextprotocol/server-puppeteer	Browser automation
Brave Search	@modelcontextprotocol/server-brave-search	Web search
Fetch	@modelcontextprotocol/server-fetch	HTTP requests
Memory	@modelcontextprotocol/server-memory	Persistent memory
Sequential Thinking	@modelcontextprotocol/server-sequential-thinking	Step-by-step reasoning

Community Servers

Server	Package/Repo	Purpose
Desktop Commander	@anthropic-ai/desktop-commander	File ops + terminals
Context7	context7-mcp	Library documentation
Obsidian	Various	Note integration
Notion	Various	Notion integration

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Comprehensive Diagnostics

When MCP servers fail, collect comprehensive diagnostic information using the bundled script:

Run Full Diagnostics

# Full system diagnostic
.\scripts\diagnose-mcp.ps1

# Diagnose specific server
.\scripts\diagnose-mcp.ps1 -ServerName "desktop-commander"

# Save report to file
.\scripts\diagnose-mcp.ps1 -OutputFile "mcp-report.md"

# JSON output for automation
.\scripts\diagnose-mcp.ps1 -Json -OutputFile "mcp-report.json"

What the Diagnostic Collects

Category	Information
System	OS version, PowerShell version, user context
Node.js	Version, path, npm path, global modules location
PATH	User PATH, session PATH, npm presence
Config	File location, validity, all configured servers
Server Details	Command, args, env vars, file existence checks
MCP Directory	Local clones, build status, node_modules presence
Processes	Claude Desktop status, running Node processes
Logs	Claude Desktop log location, recent entries, MCP errors
Issues	Automated detection with recommended fixes

Manual Information Collection

If the script isn't available, collect this information manually:

1. System Environment

# PowerShell version
$PSVersionTable | Format-List

# Node.js
node --version
(Get-Command node).Source

# npm
npm --version
npm root -g

2. Claude Desktop Config

# Config location and content
$configPath = "$env:APPDATA\Claude\claude_desktop_config.json"
Test-Path $configPath
Get-Content $configPath | ConvertFrom-Json | ConvertTo-Json -Depth 10

3. PATH Analysis

# Check for npm in PATH
$env:PATH -split ';' | Where-Object { $_ -like "*npm*" -or $_ -like "*node*" }

# User PATH (registry)
[Environment]::GetEnvironmentVariable('PATH', 'User') -split ';'

4. Test Server Manually

# For npx servers
npx.cmd -y @modelcontextprotocol/server-filesystem --help

# For local servers
node "D:/mcp/server-name/dist/index.js" --help

5. Check Claude Logs

# Find logs
Get-ChildItem "$env:APPDATA\Claude\logs" -Recurse

# View recent log
Get-Content "$env:APPDATA\Claude\logs\main.log" -Tail 50

# Search for MCP errors
Select-String -Path "$env:APPDATA\Claude\logs\*.log" -Pattern "mcp|MCP|error|ENOENT"

6. Process Information

# Claude Desktop process
Get-Process -Name "Claude" | Format-List *

# All Node processes (potential MCP servers)
Get-Process -Name "node" | ForEach-Object {
    $cmdLine = (Get-CimInstance Win32_Process -Filter "ProcessId = $($_.Id)").CommandLine
    [PSCustomObject]@{
        PID = $_.Id
        Memory = [math]::Round($_.WorkingSet64 / 1MB, 2)
        CommandLine = $cmdLine
    }
} | Format-Table -AutoSize

7. Verify File Paths

# Check all paths referenced in config
$config = Get-Content "$env:APPDATA\Claude\claude_desktop_config.json" | ConvertFrom-Json

foreach ($server in $config.mcpServers.PSObject.Properties) {
    Write-Host "`n=== $($server.Name) ===" -ForegroundColor Cyan

    # Check command
    $cmd = $server.Value.command
    Write-Host "Command: $cmd"
    Write-Host "  Exists: $(Test-Path $cmd -ErrorAction SilentlyContinue)"

    # Check args that look like paths
    foreach ($arg in $server.Value.args) {
        if ($arg -match '^[A-Za-z]:' -or $arg -match '\.(js|mjs|ts)$') {
            Write-Host "Arg: $arg"
            Write-Host "  Exists: $(Test-Path $arg)"
        }
    }
}

Information to Include in Bug Reports

When reporting MCP issues, include:

1. Diagnostic report from diagnose-mcp.ps1
2. Exact error message from Claude Desktop or logs
3. Server configuration (redact API keys)
4. Steps to reproduce
5. What you've already tried

---

Troubleshooting

Problem: MCP server not starting

Symptoms: Server shows as disabled or tools not available

Diagnostic Steps:

# 1. Check config syntax
$config = Get-Content "$env:APPDATA\Claude\claude_desktop_config.json" | ConvertFrom-Json
$config.mcpServers.'server-name'

# 2. Test command manually
node "D:/mcp/server/dist/index.js"

# 3. Check Node.js version
node --version  # Should be 18+

# 4. Check for missing dependencies
cd D:/mcp/server && npm install

Common Fixes:

• Ensure command path exists: Test-Path "C:/path/to/node.exe"
• Use forward slashes or escaped backslashes: D:/mcp or D:\\mcp
• Restart Claude Desktop completely (check Task Manager)

Problem: "spawn ENOENT" error

Cause: Command executable not found

Fix:

# Use absolute path to node
$nodePath = (Get-Command node).Source
Write-Host "Use this path: $nodePath"
# Example: C:\Program Files\nodejs\node.exe

Problem: Environment variables not available

Cause: env block not properly formatted

Fix:

{
  "mcpServers": {
    "server": {
      "command": "node",
      "args": ["server.js"],
      "env": {
        "API_KEY": "your-key-here",
        "DEBUG": "true"
      }
    }
  }
}

Problem: Server works in terminal but not in Claude

Cause: Different PATH/environment in Claude vs terminal

Fix: Use absolute paths for everything:

{
  "command": "C:/Program Files/nodejs/node.exe",
  "args": ["C:/Users/Owner/AppData/Roaming/npm/node_modules/@org/server/dist/index.js"]
}

Problem: Config file corrupted

Recovery:

# Restore from backup
$configPath = "$env:APPDATA\Claude\claude_desktop_config.json"
$backups = Get-ChildItem "$env:APPDATA\Claude\*.backup.*" | Sort-Object LastWriteTime -Descending
Copy-Item $backups[0].FullName $configPath

# Or create minimal config
@{
    mcpServers = @{}
} | ConvertTo-Json | Set-Content $configPath

---

Known Issues Prevention

Issue #1: Path escaping in JSON

Error: Invalid JSON syntax Prevention: Use forward slashes D:/mcp or double backslashes D:\\mcp

Issue #2: npx.cmd vs npx on Windows

Error: spawn npx ENOENT Prevention: Use npx.cmd on Windows:

{
  "command": "npx.cmd",
  "args": ["-y", "@package/name"]
}

Issue #3: Node version mismatch

Error: Unexpected token, SyntaxError Prevention: Verify Node 18+ is in PATH and used by Claude

Issue #4: Config edited while Claude running

Error: Config resets or corrupts Prevention: Always close Claude Desktop before editing config

Issue #5: Missing build step for cloned repos

Error: Cannot find module './dist/index.js' Prevention: Always run npm install && npm run build after cloning

---

Using Bundled Resources

Scripts (scripts/)

add-mcp-server.ps1 - Add server to Claude Desktop config

.\scripts\add-mcp-server.ps1 -Name "server-name" -Command "node" -Args @("path/to/server.js")

backup-config.ps1 - Backup Claude Desktop config

.\scripts\backup-config.ps1

Templates (templates/)

claude-desktop-config.json - Example config structure mcp-registry.json - Registry template win-cli-config.json - Win-CLI configuration template

---

Complete Setup Checklist

• Node.js 18+ installed and in PATH
• Claude Desktop installed
• Config file exists at %APPDATA%\Claude\claude_desktop_config.json
• Config file backed up
• MCP server installed (npx, npm, or clone)
• Server added to config with absolute paths
• Claude Desktop restarted
• Server tools visible in Claude
• Registry updated (if using)
• Installation logged

---

Official Documentation

• MCP Protocol: https://modelcontextprotocol.io/
• MCP Servers: https://github.com/modelcontextprotocol/servers
• Claude Desktop: https://claude.ai/download
• Desktop Commander: https://github.com/anthropics/desktop-commander

---

Package Versions (Verified 2025-12-06)

{
  "dependencies": {
    "node": ">=18.0.0",
    "@modelcontextprotocol/server-filesystem": "^0.6.x",
    "@anthropic-ai/desktop-commander": "^0.1.x"
  }
}