Claude MCP Quickstart - Expert Edition

Mental Model

An intelligent MCP (Model Context Protocol) configuration tool that sets up Claude Desktop with multiple AI servers and creates optimized development workspaces. Focuses on security-first token handling with masked display and validation.

Key Entry Points

• setup.js - Main MCP server configuration and workspace setup
• index.js - CLI interface with setup, dev-mode, verify commands
• dev-mode.js - Claude integration prompt generator
• brain-connection.js - Secure Claude brain connection orchestration (P0 security fixes)
• templates/ - Workspace templates and AI context files
• test-utils.js - Testing utilities for token security functions

Getting Started

Installation

npm install -g claude-mcp-quickstart

Quick Setup

claude-mcp-quickstart
# or
npx claude-mcp-quickstart

📋 Command Guide & Workflows

First-Time Setup Workflow

# Step 1: Configure MCP servers (required once)
npx claude-mcp-quickstart
# → Creates Claude Desktop configuration
# → Restart Claude Desktop after completion

# Step 2: Generate project integration (per project)
cd your-project
npx claude-mcp-quickstart dev-mode
# → Creates .claude-context and .claude-integration.md
# → Copy the generated prompt to Claude

# Step 3: Verify everything works
npx claude-mcp-quickstart verify
# → Checks MCP configuration status

Command Reference

Command	Purpose	Output	When to Use
npx claude-mcp-quickstart	Interactive MCP server setup	Configuration file	First time setup
npx claude-mcp-quickstart setup	Same as above	Same as above	Alternative command
npx claude-mcp-quickstart dev-mode	Generate Claude integration prompt	Long text prompt + files	In each project
npx claude-mcp-quickstart verify	Check MCP configuration	Status report	Troubleshooting
npx claude-mcp-quickstart quick-start	Setup + dev-mode combined	Setup wizard + prompt	New project setup
npx claude-mcp-quickstart --version	Show version	Version number	Version checking
npx claude-mcp-quickstart --help	Show help	Command list	Need assistance

Understanding Command Outputs

Setup Commands (npx claude-mcp-quickstart):

• Shows interactive wizard with API key prompts
• Creates/updates Claude Desktop configuration file
• Next step: Restart Claude Desktop

Dev-Mode Command (npx claude-mcp-quickstart dev-mode):

• Outputs a long integration prompt to your terminal
• Creates .claude-context and .claude-integration.md files
• Next step: Copy the terminal output and paste into Claude

Verify Command (npx claude-mcp-quickstart verify):

• Shows status of your MCP configuration
• Reports issues with setup if any
• Next step: Fix reported issues or you're ready to go

Development Setup

npm install
npm test              # Run all tests (47 brain-connection tests, 291+ total)
npm run typecheck     # TypeScript validation

🛠️ Troubleshooting

Common Issues & Solutions

Issue: "MCP servers not found in Claude"

• Cause: Claude Desktop not restarted after setup
• Fix: Completely restart Claude Desktop application

Issue: "Command not found" or "package not found"

• Cause: Package not installed or PATH issue
• Fix: Use npx claude-mcp-quickstart instead of global install

Issue: "Invalid API key" during setup

• Cause: Incorrect API key format or expired key
• Fix: Get new API key from provider links shown in setup wizard

Issue: "Permission denied" when creating config

• Cause: Claude Desktop config directory not writable
• Fix: Run with appropriate permissions or check directory ownership

Issue: "No project detected" in dev-mode

• Cause: Running dev-mode outside a project directory
• Fix: cd into your project folder first

Issue: Long prompt output in dev-mode is confusing

• Expected: This is the integration prompt for Claude
• Action: Copy the entire output and paste it into a new Claude conversation

Verification Steps

Always run these to check your setup:

npx claude-mcp-quickstart --version    # Should show current version
npx claude-mcp-quickstart verify       # Should show ✅ status messages

Getting Help

• 📋 Complete User Guide: See USER_GUIDE.md for comprehensive step-by-step instructions with 95% success rates
• 🚀 Quick Reference: This README provides command reference and troubleshooting
• 🎯 Success Metrics: USER_GUIDE.md documents validated A- grade (92/100) UX with proven completion rates
• Issues: Report bugs at GitHub Issues
• Before reporting: Include output of npx claude-mcp-quickstart verify

Architecture Overview

🚨 Critical Architecture Correction (v2.3.x)

FIXED: Major architecture understanding correction that prevents false "broken configuration" warnings for working setups.

Problem Resolved: Previous versions incorrectly treated Claude Desktop's built-in tools (Filesystem, Context7, GitHub) as MCP servers, causing false positive errors for users with properly configured systems.

Solution: System now correctly distinguishes:

• Built-in Extensions: Filesystem, Context7 (Settings → Extensions)
• Built-in Connectors: GitHub (Settings → Connectors)
• Custom MCP Servers: memory, supabase, brave, tavily (managed via claude_desktop_config.json)

Current Architecture (Post-Correction)

Built-in Claude Desktop Features (managed via Settings UI):

• Filesystem Access: Settings → Extensions → Filesystem
• Documentation/Context: Settings → Extensions → Context7
• GitHub Integration: Settings → Connectors → GitHub

Custom MCP Servers (managed via configuration file):

• Memory: Conversation memory persistence (core server)
• Supabase: Database operations with access tokens
• Brave Search: Web search capabilities
• Tavily AI: AI-optimized search

Token Security System

• Masked Display: Shows first 5 + last 3 characters (abcde********123)
• Memory Clearing: Automatic token cleanup after use
• Format Validation: Regex patterns for GitHub, Supabase, Brave, Tavily
• UX Workflow: Enter (keep) / "-" (delete) / new value (replace)

Validation Strategy

• Built-in Tools: Tested through direct Claude tool calls (no MCP config validation)
• Custom MCP Servers: Validated through MCP configuration and server responses
• Troubleshooting: Directs users to correct Settings sections for built-in features

Workspace Creation

• Lovable.dev Integration: Full-stack development templates
• AI Context Files: Specialized prompts and patterns
• Project Templates: Customized by development type
• Bootstrap Lovable v2: Framework integration

Project Structure

claude-mcp-quickstart/
├── README.md           # This file
├── CLAUDE.md           # Development guidelines
├── CHANGELOG.md        # Version history and changes
├── MIGRATION.md        # Migration guide for existing users
├── ARCHITECTURE.md     # Claude Desktop architecture reference
├── TEST_ARCHITECTURE.md # Test suite architecture and REQ-402 refactoring documentation
├── docs/TESTING_PATTERNS.md # Quick reference for modern testing patterns
├── package.json        # NPM configuration
├── index.js           # CLI entry point
├── setup.js           # Main setup logic & token security
├── dev-mode.js        # Claude integration prompt generator
├── brain-connection.js # Secure brain connection with P0 security fixes
├── test-utils.js      # Security testing utilities
├── templates/         # Workspace templates
│   ├── ai-activation.md
│   ├── usage-guide.md
│   ├── prompt-library.md
│   ├── lovable-patterns.md
│   └── project-templates/
├── *.spec.js          # Test files (291 tests)
├── vitest.config.js   # Test configuration & Windows compatibility  
├── .prettierrc        # Code formatting rules
└── eslint.config.js   # Code linting configuration

New Development Workflow

The refactored version introduces a streamlined development workflow:

1. Setup Phase: Run claude-mcp-quickstart to configure MCP servers
2. Integration Phase: Run claude-mcp-quickstart dev-mode to generate Claude integration prompts
3. Development Phase: Use the generated prompts to establish workspace context with Claude

Why This Change?

• Built-in Connectors: Claude now provides native GitHub and filesystem connectors that work better than external MCP servers
• Enhanced Security: Native extensions offer improved access control and security models
• Better Performance: Native connectors eliminate external process overhead and provide faster response times
• Simplified Setup: Fewer external dependencies to manage, configure, and troubleshoot
• Future-Proof: Migration path ensures compatibility with Claude's evolving feature set

Dev-Mode Tool Features

The refactored dev-mode.js now:

• Detects project type automatically (React, Next.js, Vue, Python, Rust, etc.)
• Generates workspace context with project structure and available MCP tools
• Creates integration prompts that Claude can use to understand your setup
• Writes context files (.claude-context, .claude-integration.md) for future reference

Usage Example

cd your-project
claude-mcp-quickstart dev-mode
# Copy the generated prompt and paste it to Claude

The tool generates a comprehensive prompt that tells Claude:

• Your project directory and type
• Available MCP servers and their capabilities
• Suggested commands and workflows
• Context to save to memory for future sessions

Migration for Existing Users

If you're upgrading from a previous version:

1. Graceful Deprecation: When running claude-mcp-quickstart setup, deprecated servers (GitHub/Filesystem) will show confirmation prompts
2. Choose Your Path: You can continue using deprecated servers (discouraged) or migrate to Claude Settings
3. Recommended Migration:
   • GitHub: Go to Claude Settings → Connectors → GitHub for better performance and native integration
   • Filesystem: Go to Claude Settings → Extensions → Filesystem for improved security and file access control
   • Context7: Go to Claude Settings → Extensions for documentation and context features
4. No Forced Changes: Existing configurations remain functional while you decide when to migrate

Deprecation Approach

This package implements a graceful deprecation strategy that prioritizes user choice and backward compatibility:

What You'll See

• ⚠️ Deprecation Warnings: Clear messages explaining why native alternatives are better
• Confirmation Prompts: Choose whether to proceed with deprecated servers or migrate
• Migration Guidance: Step-by-step instructions for using Claude Settings
• Performance Benefits: Explanations of why native connectors are superior

No Breaking Changes

• Existing configurations preserved - your current setup continues working
• Optional migration - upgrade when you're ready, not when we force it
• Clear benefits explained - understand why migration improves your experience

Example Experience

⚠️  GitHub MCP Server is deprecated!
Recommended: Use Claude Settings → Connectors → GitHub instead
This provides better performance and native integration.

? Continue with deprecated GitHub MCP server anyway? (y/N)

Security Features

• 🚨 Template Injection Protection (P0 Fix): All user inputs in brain-connection module properly escaped to prevent code execution
• Input Sanitization: Comprehensive HTML/markdown escaping for projectPath, projectType, and mcpServers
• XSS Prevention: Generated markdown files secured against script injection attacks
• Token Security: Memory clearing after use and masked display during input
• Input Validation: Regex patterns for GitHub, Supabase, Brave, and Tavily tokens
• Error Boundaries: Structured exception handling prevents crashes from malformed data
• JSON Validation: Robust parsing with fallback behavior for status files
• Deprecation Safety: Confirmation prompts before proceeding with deprecated servers
• Configuration Protection: Atomic file writes and JSON parsing with error recovery
• Migration Security: Existing tokens preserved during configuration updates
• Comprehensive Testing: 291+ tests covering architectural validation, security patterns, injection prevention, capability counting systems, and reliability flows

Development

Prerequisites

• Node.js 18+ (tested on 18, 20)
• npm or npx

Development Scripts

npm test              # Run tests in watch mode
npm run test:run      # Run tests once
npm run lint          # Check code quality with ESLint
npm run format        # Format code with Prettier
npm run format:check  # Verify code formatting

Cross-Platform Testing

This package is tested on:

• ✅ Ubuntu Latest (Node.js 18, 20)
• ✅ macOS Latest (Node.js 18, 20)
• ✅ Windows Latest (Node.js 18, 20)

Windows compatibility is ensured through a custom Vite plugin that handles shebang lines in the test environment.

Code Quality

• Prettier for consistent formatting
• ESLint for code quality
• 291+ comprehensive tests including 47 brain-connection tests covering architectural validation, security injection prevention, and capability counting systems
• Vitest for fast, modern testing
• Security-First Testing: Dedicated test suite for template injection, XSS prevention, and error boundaries

Troubleshooting CI Issues

If you encounter Windows CI failures:

• Path issues: Use filename checks instead of full path assertions in tests
• Shell issues: Add shell: bash to GitHub Actions steps that use wildcards or Unix commands
• Debug command: Use gh run view <run-id> --log-failed to see detailed failure logs

Publishing

Manual Publishing

The repository includes a manual publishing workflow for controlled NPM releases:

# Navigate to Actions tab on GitHub
# Select "NPM Publish" workflow  
# Click "Run workflow" and configure:

Workflow Options:

• Version Type: patch (1.0.1), minor (1.1.0), or major (2.0.0)
• Registry: npm (npmjs.com) or github (GitHub Packages)
• Dry Run: Test the workflow without actually publishing

Publishing Process:

1. Quality Gate - Runs full test suite across all platforms
2. Version Bump - Auto-increments package.json version
3. Duplicate Check - Prevents publishing existing versions
4. Publish - Pushes package to selected registry
5. Git Tagging - Creates release tags and GitHub releases

Required Secrets

For NPM publishing, add this GitHub repository secret:

• NPM_AUTH_TOKEN - Your NPM authentication token

GitHub Packages publishing uses the built-in GITHUB_TOKEN.

⚠️ Security Notes:

• Never enable GitHub Actions debug logging (ACTIONS_STEP_DEBUG) for publishing workflows
• NPM tokens are automatically masked in workflow logs for security
• Tokens are only used during the publishing step and are not persisted

Publishing Safety Features

• ✅ Cross-platform testing before publish
• ✅ Automatic version conflict detection
• ✅ Dry-run mode for testing
• ✅ Git tagging with release notes
• ✅ Rollback protection via version checks

First-Time Publishing Setup

Step 1: Create NPM Token

1. Log in to npmjs.com
2. Go to Access Tokens → Generate New Token
3. Select "Automation" token type for CI/CD
4. Copy the token (starts with npm_)

Step 2: Add GitHub Secret

1. Go to your repository → Settings → Secrets and variables → Actions
2. Click "New repository secret"
3. Name: NPM_AUTH_TOKEN
4. Value: Your NPM token from Step 1
5. Click "Add secret"

Step 3: First Publish

1. Navigate to Actions tab → "NPM Publish" workflow
2. Click "Run workflow" → Select options → "Run workflow"
3. Monitor the workflow execution for any issues

Troubleshooting

Common Issues:

• "Version already exists": The workflow automatically detects and skips duplicate versions. This is normal behavior, not an error.

• "NPM_AUTH_TOKEN not found": Verify the secret is added to your repository with the exact name NPM_AUTH_TOKEN.

• "Quality gate failed": Ensure all tests pass locally before publishing:

  npm run test:run
  npm run lint  
  npm run format:check

• "Git push failed": Check repository permissions. The workflow needs contents: write permission.

Getting Help:

• Check workflow logs in the Actions tab for detailed error messages
• Verify your NPM token has publish permissions for your package
• Ensure package.json name field matches your NPM package name

📚 Complete Documentation System

This project implements a comprehensive development workflow system documented in the following guides:

Core Documentation

• CLAUDE.md - Core principles, TDD enforcement, and QShortcuts workflow
• docs/COMPLETE_SYSTEM_INTEGRATION.md - Master integration guide

Implementation Guides

• docs/DEVELOPER_WORKFLOW_GUIDE.md - Step-by-step feature development tutorials
• docs/TESTING_FRAMEWORK_GUIDE.md - 11-point testing checklist with property-based examples
• docs/AGENT_SYSTEM_GUIDE.md - Complete agent coordination documentation
• docs/TROUBLESHOOTING_GUIDE.md - Common issues and solutions

Reference Documentation

• CHANGELOG.md - Version history and changes
• MIGRATION.md - Migration guide for existing users
• ARCHITECTURE.md - Claude Desktop architecture reference
• TEST_ARCHITECTURE.md - Test suite architecture and REQ-402 refactoring

Quick Start for Developers

1. New to the system? Start with docs/DEVELOPER_WORKFLOW_GUIDE.md
2. Want to understand testing? Read docs/TESTING_FRAMEWORK_GUIDE.md
3. Need agent coordination? See docs/AGENT_SYSTEM_GUIDE.md
4. Having issues? Check docs/TROUBLESHOOTING_GUIDE.md

The complete documentation integrates TDD enforcement, requirements discipline, agent coordination, and quality gates into a cohesive development system.