Mastering Claude Code: Skills, Subagents, and MCP Deep Dive

Introduction

Claude Code has evolved from a simple AI coding assistant to a sophisticated agentic development platform. Three features set it apart: Skills (task-specific modules), Subagents (parallel AI workers), and MCP (Model Context Protocol for tool integration).

Let's dive deep into each of these power features.

Part 1: Skills - Task-Specific Intelligence

Skills in Claude Code are specialized instruction sets that activate for specific tasks. Think of them as modes that give Claude focused expertise and workflows.

Understanding Skills

# List available skills
claude /help

# Common built-in skills
/commit     # Smart git commits with context
/review     # Code review current changes
/test       # Run and analyze tests
/plan       # Create implementation plans
/fix        # Fix identified issues

How Skills Work

When you invoke a skill, Claude Code:

1. Loads skill-specific instructions
2. Adjusts its behavior and focus
3. Uses appropriate tools and patterns
4. Follows skill-defined workflows

# Example: /commit skill behavior

1. Analyzes staged changes with git diff
2. Reviews recent commit history for style
3. Understands the semantic meaning of changes
4. Generates appropriate commit message
5. Follows conventional commit format
6. Includes relevant context and reasoning

Built-in Skills Deep Dive

/commit - Smart Git Commits

# Stage your changes
git add .

# Let Claude analyze and commit
claude /commit

# Claude will:
# 1. Read all staged changes
# 2. Understand the purpose of changes
# 3. Generate semantic commit message
# 4. Create the commit

Example output:

Analyzing staged changes...
- Modified: src/auth/login.ts (added rate limiting)
- Modified: src/auth/login.test.ts (added rate limit tests)
- Added: src/middleware/rateLimit.ts (new rate limiter)

Generating commit message...

feat(auth): add rate limiting to login endpoint

- Implement sliding window rate limiter middleware
- Add 5 attempts per minute limit for login
- Include bypass for whitelisted IPs
- Add comprehensive test coverage

Commit created: a1b2c3d

/review - Code Review

# Review current changes
claude /review

# Review specific files
claude /review src/auth/*.ts

# Review with focus areas
claude "review for security vulnerabilities"

/plan - Implementation Planning

# Create implementation plan
claude /plan "add user profile feature"

# Claude outputs:
# 1. Requirements analysis
# 2. Affected files identification
# 3. Step-by-step implementation plan
# 4. Testing strategy
# 5. Risk assessment

Creating Custom Skills

You can define custom skills in your CLAUDE.md file:

# CLAUDE.md

## Custom Skills

### /deploy
When I say /deploy, follow this workflow:
1. Run all tests: `npm test`
2. Build production: `npm run build`
3. Run type check: `npm run type-check`
4. If all pass, run: `./scripts/deploy.sh`
5. Verify deployment at https://api.myapp.com/health
6. Report status

### /db-migrate
When I say /db-migrate:
1. Show pending migrations: `npx prisma migrate status`
2. Ask for confirmation before applying
3. Run migrations: `npx prisma migrate deploy`
4. Regenerate client: `npx prisma generate`
5. Run migration tests

### /security-check
When I say /security-check:
1. Run npm audit: `npm audit`
2. Check for secrets in code: `git secrets --scan`
3. Run SAST scanner: `semgrep --config=auto`
4. Summarize findings by severity
5. Suggest fixes for critical issues

Skill Best Practices

1. Make skills atomic: Each skill should do one thing well
2. Include validation steps: Verify success at each stage
3. Handle errors gracefully: Define what to do when things fail
4. Document expectations: Clear descriptions of inputs/outputs

Part 2: Subagents - Parallel AI Execution

Subagents are specialized AI instances that Claude Code can spawn to handle subtasks in parallel. They're game-changing for complex workflows.

How Subagents Work

Main Claude Session
        |
        ├── Spawns Subagent A (code review)
        │        └── Works on auth module
        │
        ├── Spawns Subagent B (test writing)
        │        └── Writes unit tests
        │
        └── Spawns Subagent C (documentation)
                 └── Updates API docs

All subagents work in parallel, report back to main session

Subagent Types

Claude Code includes several specialized subagent types:

1. Explore Agent

Fast codebase exploration:

# Claude can spawn an explore agent internally
"Search the codebase for all authentication-related files"

# Explore agent:
# - Uses optimized file search
# - Understands code patterns
# - Returns relevant findings quickly

2. Code Reviewer Agent

Dedicated code review:

# Automatically spawned for thorough reviews
"Review this PR for security issues"

# Reviewer agent:
# - Checks for OWASP vulnerabilities
# - Validates input handling
# - Reviews authentication flows
# - Reports findings by severity

3. Test Writer Agent

Specialized test generation:

"Generate comprehensive tests for the user service"

# Test writer agent:
# - Analyzes code coverage gaps
# - Generates unit tests
# - Creates integration tests
# - Follows existing test patterns

4. Planner Agent

Implementation planning:

"Plan the implementation of a new payment system"

# Planner agent:
# - Analyzes requirements
# - Identifies dependencies
# - Creates phased plan
# - Estimates complexity

Subagent Execution Patterns

Parallel Independent Tasks

// Conceptual representation
async function handleComplexTask() {
  // Spawn subagents for independent tasks
  const results = await Promise.all([
    spawnSubagent('reviewer', 'Review auth module'),
    spawnSubagent('tester', 'Write auth tests'),
    spawnSubagent('documenter', 'Update auth docs'),
  ]);

  // Aggregate and act on results
  return synthesizeResults(results);
}

Sequential with Handoff

// One subagent's output feeds the next
async function sequentialWorkflow() {
  // 1. Planner analyzes and creates plan
  const plan = await spawnSubagent('planner', 'Plan feature X');

  // 2. Implementer executes the plan
  const code = await spawnSubagent('implementer', plan);

  // 3. Reviewer checks the implementation
  const review = await spawnSubagent('reviewer', code);

  // 4. Fix any issues found
  if (review.issues.length > 0) {
    await spawnSubagent('fixer', review.issues);
  }
}

Subagent Configuration

Configure subagent behavior in settings:

{
  "subagents": {
    "maxConcurrent": 3,
    "timeout": 300000,
    "models": {
      "explore": "haiku",
      "reviewer": "sonnet",
      "planner": "opus"
    }
  }
}

When to Use Subagents

Good use cases:

• Large codebase exploration
• Multi-file refactoring
• Comprehensive code review
• Parallel test generation
• Documentation updates

When main agent is better:

• Simple, linear tasks
• Quick fixes
• Single-file changes
• Interactive conversations

Part 3: MCP - Model Context Protocol

MCP (Model Context Protocol) is a universal connector that lets Claude Code interact with external tools, services, and data sources through a standardized interface.

Understanding MCP

Think of MCP as USB for AI tools—a standard protocol that lets any tool connect to any AI agent:

┌─────────────┐       ┌─────────────┐
│ Claude Code │──MCP──│   GitHub    │
└─────────────┘       └─────────────┘
       │
       │              ┌─────────────┐
       └───────MCP────│  Database   │
       │              └─────────────┘
       │              ┌─────────────┐
       └───────MCP────│   Slack     │
                      └─────────────┘

MCP Architecture

Claude Code (Client)
       │
       ▼
┌──────────────┐
│ MCP Protocol │
└──────────────┘
       │
       ▼
┌──────────────┐     ┌──────────────┐     ┌──────────────┐
│ MCP Server 1 │     │ MCP Server 2 │     │ MCP Server 3 │
│   (GitHub)   │     │  (Postgres)  │     │    (Jira)    │
└──────────────┘     └──────────────┘     └──────────────┘
       │                    │                    │
       ▼                    ▼                    ▼
   GitHub API          PostgreSQL            Jira API

Configuring MCP Servers

Add MCP servers in your settings:

{
  "mcpServers": {
    "github": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-github"],
      "env": {
        "GITHUB_PERSONAL_ACCESS_TOKEN": "ghp_xxxx"
      }
    },
    "postgres": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-postgres"],
      "env": {
        "DATABASE_URL": "postgresql://localhost/mydb"
      }
    },
    "filesystem": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-filesystem"],
      "args": ["/allowed/path1", "/allowed/path2"]
    }
  }
}

Popular MCP Servers

1. GitHub MCP Server

# Install
npm install -g @modelcontextprotocol/server-github

# Capabilities:
# - Create/read/update issues
# - Manage pull requests
# - Access repository content
# - Search code across repos

Usage with Claude:

claude "create a GitHub issue for the login bug we discussed"
# Claude uses MCP to:
# 1. Connect to GitHub
# 2. Create issue with full context
# 3. Link related PRs
# 4. Assign and label appropriately

2. Database MCP Server

# PostgreSQL server
npm install -g @modelcontextprotocol/server-postgres

# Capabilities:
# - Query databases
# - Describe schemas
# - Understand relationships
# - Generate migrations

Usage:

claude "analyze the users table and suggest indexes"
# Claude uses MCP to:
# 1. Query table structure
# 2. Analyze query patterns
# 3. Recommend optimizations

3. Slack MCP Server

npm install -g @modelcontextprotocol/server-slack

# Capabilities:
# - Read channels
# - Post messages
# - Search conversations
# - Manage threads

4. Memory MCP Server

npm install -g @modelcontextprotocol/server-memory

# Capabilities:
# - Persistent memory across sessions
# - Store project context
# - Remember decisions
# - Track progress

Building Custom MCP Servers

Create your own MCP server for custom integrations:

// my-custom-mcp-server/index.ts
import { Server } from "@modelcontextprotocol/sdk/server";
import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio";

const server = new Server({
  name: "my-custom-server",
  version: "1.0.0",
});

// Define available tools
server.setRequestHandler("tools/list", async () => ({
  tools: [
    {
      name: "deploy_to_staging",
      description: "Deploy the current branch to staging",
      inputSchema: {
        type: "object",
        properties: {
          branch: { type: "string" },
          skipTests: { type: "boolean", default: false },
        },
        required: ["branch"],
      },
    },
  ],
}));

// Handle tool execution
server.setRequestHandler("tools/call", async (request) => {
  const { name, arguments: args } = request.params;

  if (name === "deploy_to_staging") {
    // Your deployment logic
    const result = await deployToStaging(args.branch, args.skipTests);
    return { content: [{ type: "text", text: result }] };
  }
});

// Start server
const transport = new StdioServerTransport();
await server.connect(transport);

MCP Best Practices

1. Principle of Least Privilege

{
  "mcpServers": {
    "github": {
      "env": {
        "GITHUB_TOKEN": "token_with_minimal_scopes"
      }
    }
  }
}

2. Sandbox External Operations

{
  "mcpServers": {
    "filesystem": {
      "args": ["/project/root"],  // Restrict to project
      "sandbox": true
    }
  }
}

3. Audit MCP Usage

# Review what MCP servers have done
claude "show me recent MCP operations"

Putting It All Together

Here's a real-world workflow using Skills, Subagents, and MCP:

Scenario: Implementing a Feature with Full CI/CD

# 1. Start with planning skill
claude /plan "implement user notifications feature"

# Claude spawns planner subagent, uses MCP to:
# - Read existing code patterns
# - Check related GitHub issues
# - Query database schema

# 2. Implementation with parallel subagents
# Claude automatically:
# - Spawns implementer for notification service
# - Spawns implementer for email templates
# - Spawns implementer for API endpoints
# All working in parallel

# 3. Review skill
claude /review

# Spawns reviewer subagent that:
# - Checks code quality
# - Validates security
# - Ensures test coverage

# 4. Commit skill
claude /commit

# Uses MCP GitHub server to:
# - Create semantic commit
# - Push to branch
# - Create pull request
# - Link to related issue

# 5. Custom deploy skill
claude /deploy-staging

# Uses custom MCP server to:
# - Run deployment pipeline
# - Run smoke tests
# - Post status to Slack

Conclusion

Claude Code's power lies in the synergy of these three features:

• Skills provide focused expertise for specific tasks
• Subagents enable parallel, specialized work
• MCP connects Claude to your entire toolchain

Together, they transform Claude Code from a coding assistant into a complete agentic development platform that can handle complex, multi-step workflows autonomously while maintaining the control and oversight you need.

Start by mastering the built-in skills, experiment with subagents for complex tasks, and gradually add MCP integrations to connect Claude to your development ecosystem.

The future of software development is agentic—and Claude Code is leading the way.

Want to optimize your Claude Code setup? Schedule a consultation to discuss advanced configurations.