Claude Code Guide

This comprehensive guide covers every discoverable Claude Code command as of June 2025,
including many features that are not widely known or documented in basic tutorials.

This represents the most complete Claude Code command reference available.

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For updates and contributions, visit the official Claude Code documentation

Visit: https://zebbern.github.io/ for more detailed info!

Section	Status
Guides on how to install on Windows, Linux, MacOS	✅
Tips and Tricks	✅
MCP Overview with what to use	✅
Community Guides	✅
Troubleshooting	✅
How to use Claude code the most optimal way	✅

I Usually Start my Claude with Claude --dangerously-skip-permissions only use this if you know exactly what ur doing!

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Quick Start

# Quick Installment

## Method 1 – NPM (global) ⭐️ Official
npm install -g @anthropic-ai/claude-code
# Requires Node 18+ on macOS / Linux / WSL :contentReference[oaicite:0]{index=0}

## Method 2 – Homebrew Tap (macOS & Linux) *️⃣
brew install anthropic/tap/claude-code
# Formula contributed by the community :contentReference[oaicite:1]{index=1}

## Method 3 – Arch Linux AUR *️⃣
yay -S claude-code        # or paru -S claude-code
# Keeps pace with npm releases :contentReference[oaicite:2]{index=2}

## Method 4 – Docker (containerised) *️⃣
docker pull ghcr.io/rchgrav/claudebox:latest
docker run -it -v "$PWD":"$PWD" -w "$PWD" \
ghcr.io/rchgrav/claudebox:latest
# Nice when you can’t touch the host system :contentReference[oaicite:3]{index=3}

## Method 5 – Windows via WSL (Anthropic-recommended path)
# 1) Enable WSL 2 and install Ubuntu
# 2) Inside Ubuntu:
sudo apt update && sudo apt install -y nodejs npm
npm install -g @anthropic-ai/claude-code
# Step-by-step guide :contentReference[oaicite:4]{index=4}

## Method 6 – Build from source (any OS) *️⃣
git clone https://github.com/anthropics/claude-code.git
cd claude-code && pnpm install && pnpm build
pnpm --filter cli run cli:install
# Handy for cutting-edge commits or local patches :contentReference[oaicite:5]{index=5}

# Interactive Mode
claude                      # Start interactive REPL
claude "your question"      # Start with initial prompt

# One-Shot Mode  
claude -p "analyze this"    # Quick query and exit
cat file | claude -p "fix"  # Process piped content

# Management
claude config              # Configure settings
claude update              # Update to latest
claude mcp                 # Setup MCP servers

🚀 Installation & Setup

System Requirements:

• Node.js 16+ or standalone binary
• API key from Anthropic
• 4GB RAM minimum (8GB+ recommended for large projects)
• Internet connection for API calls

Supported Platforms:

• macOS (Intel/Apple Silicon)
• Linux (Ubuntu 18+, Debian 10+, CentOS 7+)
• Windows 10/11 (WSL recommended)

Installation Methods

Method 1: NPM Installation (Verified ✅)

# Install globally - CORRECT PACKAGE NAME
npm install -g @anthropic-ai/claude-code

# Verify installation
claude --version

Initial Setup

1. API Key Configuration (Verified ✅)

# Required: Get your API key from https://console.anthropic.com
export ANTHROPIC_API_KEY="sk-your-key-here"

# Make permanent (choose your shell)
# Bash
echo 'export ANTHROPIC_API_KEY="sk-your-key-here"' >> ~/.bashrc
source ~/.bashrc

# Zsh
echo 'export ANTHROPIC_API_KEY="sk-your-key-here"' >> ~/.zshrc
source ~/.zshrc

# Fish
echo 'set -gx ANTHROPIC_API_KEY "sk-your-key-here"' >> ~/.config/fish/config.fish

2. Basic Configuration (Mostly Verified ✅)

# Interactive setup
claude config

# Set basic defaults 
claude config set -g model claude-sonnet-4
claude config set -g verbose true
claude config set -g outputFormat text

# Test installation
claude "Hello, Claude!"
claude /doctor  

3. Settings i Turn Off

export DISABLE_TELEMETRY=1
export DISABLE_ERROR_REPORTING=1
export DISABLE_NON_ESSENTIAL_MODEL_CALLS=1


# Security defaults
claude config set allowedTools "Edit,View"
claude config set hasTrustDialogAccepted
claude config set hasCompletedProjectOnboarding 
claude config set ignorePatterns
claude config set --global

Health Check & Testing

# Basic functionality test 
claude "Explain what you can do"

# Print mode test 
claude -p "What is 2+2?"

# Tool permission test
claude "Create a file called test.txt with 'Hello World'"
# Should prompt for Edit permission

# Session continuity test  
claude -c  # Should continue from previous session

health check

claude /doctor
Expected output might include:
# ✅ API Key: Valid
# ✅ Network: Connected  
# ✅ Model Access: Available

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🔌 MCP Integration

Understanding MCP (Model Context Protocol)

What is MCP? MCP extends Claude's capabilities by connecting to external services, databases, APIs, and tools.

MCP Architecture:

Claude Code ←→ MCP Protocol ←→ MCP Servers ←→ External Services

MCP Setup & Configuration

Basic MCP Commands

claude mcp                    # Interactive MCP configuration
claude mcp list              # List configured servers             # Check server health
claude mcp add <name> <cmd>  # Add new server
claude mcp remove <name>     # Remove server

MCP Configuration File

Location:~/.claude.json

Scope-Based Configuration Files

User/Global Scope: Global MCP servers are configured in ~/.claude-code/mcp/global.json Project Scope: Project-scoped servers are stored in a .mcp.json file at your project's root directory

{
  "mcpServers": {
    "git": {
      "command": "git-mcp-server",
      "args": [],
      "env": {}
    },
    "postgres": {
      "command": "postgres-mcp-server", 
      "args": ["--host", "localhost", "--port", "5432"],
      "env": {
        "POSTGRES_USER": "developer",
        "POSTGRES_PASSWORD": "dev_password",
        "POSTGRES_DB": "myapp_development"
      }
    }
  }
}

MCP Servers

Note: The exact package names and installation commands below may not be accurate. Consult official MCP documentation for current server packages.

Development Tools

# npm install -g git-mcp-server         

# claude mcp add git "git-mcp-server"
# claude mcp add github "github-mcp-server --token $GITHUB_TOKEN"

Database Integration

npm install -g postgres-mcp-server               
npm install -g mysql-mcp-server                  
npm install -g sqlite-mcp-server               

# Setup examples
# export POSTGRES_URL="postgresql://user:password@localhost:5432/mydb"
# claude mcp add postgres "postgres-mcp-server --url $POSTGRES_URL"

MCP Tool Permissions

# Allow specific MCP tools 
claude --allowedTools "mcp__git__commit,mcp__git__push"

# Allow all tools from specific server
claude --allowedTools "mcp__postgres__*"

# Combined with built-in tools
claude --allowedTools "Edit,View,mcp__git__*"

---

⌨️ Commands Reference

CLI Commands

Core Commands

Command	Description	Example	Status
claude	Start interactive REPL	claude
claude "query"	REPL with initial prompt	claude "help debug this"
claude -p "query"	One-shot query (print mode)	claude -p "explain function"

Session Management

Command	Description	Example	Status
claude -c	Continue last session	claude -c
claude -r <id>	Resume specific session	claude -r abc123
claude --resume <name>	Resume named session	claude --resume project-review

Configuration Management

Command	Description	Example	Status
claude config	Interactive configuration	claude config
claude config list	List all settings	claude config list
claude config get <key>	Get specific value	claude config get model
claude config set <key> <value>	Set value	claude config set model sonnet

CLI Flags & Options

Essential Flags

Flag	Short	Description	Example
--print	-p	Print response without interactive mode	claude -p "help"
--continue	-c	Load most recent conversation	claude -c
--help	-h	Show help information	claude --help
--version	-v	Show version	claude --version

Output Control Flags

Flag	Options	Description	Example
--output-format	text, json, stream-json	Control response format	claude -p "help" --output-format json
--json	-	Shorthand for JSON output	claude -p "analyze" --json

Security & Permission Flags

Flag	Risk Level	Description	Example
--allowedTools <tools>	LOW	Whitelist specific tools	claude --allowedTools "Edit,View"
--disallowedTools <tools>	LOW	Blacklist specific tools	claude --disallowedTools "Bash"
--dangerously-skip-permissions	CRITICAL	Skip ALL permission prompts	claude --dangerously-skip-permissions

Advanced Flags

Flag	Purpose	Example	Notes
--add-dir <path>	Add working directories	claude --add-dir ../lib ../src
--model <model>	Set specific model	claude --model sonnet
--verbose	Enable detailed logging	claude --verbose

Slash Commands (Interactive Mode)

Commands

Command	Purpose	Status
/help	Show all slash commands
/clear	Clear current conversation
/exit	Exit Claude safely
/bug	Report issues

Commands

/doctor        # Complete health check
/status        # System information  
/cost          # Token usage stats
/config        # Configuration menu
/permissions   # Manage tool access
/memory        # Edit memory files
/sessions      # List all sessions

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⚙️ Configuration

Configuration System Overview

Claude Code uses a hierarchical configuration system:

1. Command-line flags (highest priority)
2. Environment variables
3. Project configuration (location may vary)
4. Global configuration (likely ~/.claude.json)
5. Built-in defaults (lowest priority)

Configuration Files

Global Configuration

Location: ~/.claude.json

{
  "model": "claude-sonnet-4",
  "verbose": true,
  "outputFormat": "text", 
  "allowedTools": ["Edit", "View"],
  "disallowedTools": [],
}

Project Configuration

Location: settings.json OR similar

{
  "model": "claude-sonnet-4",
  "systemPrompt": "You are a senior developer working on this project",
  "allowedTools": [
    "Edit",
    "View",
    "Bash(git:*)",
    "Bash(npm:*)"
  ],
}

Environment Variables

Core Variables

Variable	Required	Purpose	Example
ANTHROPIC_API_KEY	YES	API Authentication	sk-ant-api03-xxx
ANTHROPIC_MODEL	No	Default model	claude-sonnet-4
ANTHROPIC_BASE_URL	No	API endpoint override	https://api.anthropic.com

Variables

export DISABLE_NON_ESSENTIAL_MODEL_CALLS=1  
export MAX_THINKING_TOKENS=50000
export DISABLE_TELEMETRY=1


# Cloud provider variables
export CLAUDE_CODE_USE_BEDROCK=1
export CLAUDE_CODE_USE_VERTEX=1

Network & Proxy

# Standard proxy variables
export HTTP_PROXY="http://proxy.company.com:8080"
export HTTPS_PROXY="https://proxy.company.com:8443"  
export NO_PROXY="localhost,127.0.0.1,*.company.com"

---

Security & Permissions

Permission System

How it works:

• Claude asks for permission before using tools
• Permissions are remembered per session
• Dangerous operations require confirmation

Permission Levels

Level	Description	Risk	Use Case
Interactive	Prompt for each operation	Low	Development work
Allowlist	Pre-approved tools only	Medium	Automation scripts
Dangerous	Skip all permissions	CRITICAL	Containers only

Tool Permission Patterns

# Allow specific tools
claude --allowedTools "Edit,View"

# Allow tool categories  
claude --allowedTools "Edit,View,Bash"

# Scoped permissions (Git operations only)
claude --allowedTools "Bash(git:*)"

# Multiple scopes
claude --allowedTools "Bash(git:*),Bash(npm:*)"

Dangerous Mode (CRITICAL Security Feature)

# DANGEROUS - Can cause data loss
claude --dangerously-skip-permissions

# Only use in isolated environments:
# ✅ Safe: Isolated Docker container  
# ❌ NEVER: Production systems, shared machines, systems with important data

Security Best Practices

1. Start Restrictive

# Good: Specific permissions
claude --allowedTools "Edit,View,Bash(git:status)"

# Bad: Broad permissions  
claude --allowedTools "Bash"

2. Protect Sensitive Data

# Good: Environment variables
export DATABASE_URL="postgresql://user:pass@host/db"

# Bad: Hardcoded credentials in commands
# claude "connect to postgresql://user:password123@host/db"

3. Regular Security Audits

# Check current permissions
claude config get allowedTools
claude config get disallowedTools

# Review configuration
claude config list

---

🤖 Automation & Scripting

CI/CD Integration

GitHub Actions Example

name: Claude Code Review
on:
  pull_request:
    branches: [main, develop]

jobs:
  claude-review:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Setup Node.js
        uses: actions/setup-node@v4
        with:
          node-version: '18'
      - name: Install Claude Code
        run: npm install -g @anthropic-ai/claude-code
      - name: Run Review
        env:
          ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}
        run: |
          claude -p "Review changes for security issues and bugs" \
            --allowedTools "View" \
            --output-format json > review-results.json

Automation Scripts

Pre-commit Hook Example

#!/bin/bash
# .git/hooks/pre-commit

# Get staged files
staged_files=$(git diff --cached --name-only --diff-filter=ACM)

if [ -z "$staged_files" ]; then
    exit 0
fi

# Analyze with Claude
analysis=$(echo "$staged_files" | xargs cat | \
    claude -p "Review these changes for issues before commit" \
    --allowedTools "View" \
    --output-format json)

# Check for critical issues
if echo "$analysis" | jq -e '.critical_issues[]' > /dev/null 2>&1; then
    echo "❌ Critical issues found - commit blocked"
    exit 1
fi

echo "✅ Code analysis passed"

---

🔧 Troubleshooting

Diagnostic Commands

# Basic health checks
claude --version             
claude --help                   
claude config list                 
claude /doctor                  

Common Issues & Solutions

1. Authentication Issues

# Check API key
echo $ANTHROPIC_API_KEY

# Test connection
claude -p "test" --verbose

# Reset authentication 

2. Installation Issues

# Reinstall
npm uninstall -g @anthropic-ai/claude-code     
npm install -g @anthropic-ai/claude-code      

# Check Node.js version
node --version  # Should be 16+

3. Permission Issues

# Check current permissions
claude config get allowedTools

# Reset permissions
claude config set allowedTools "[]"
claude config set allowedTools '["Edit", "View"]'

4. MCP Issues

# Debug MCP 
claude --mcp-debug
claude mcp status  
claude mcp restart --all

Debug Mode

# Enable verbose logging
claude --verbose

# Check logs (verify log location)

---

🚀 Advanced Features

Context Management

CLAUDE.md - Project Memory

Purpose: Store persistent project information that Claude remembers

Location: Project root directory

# Project: My Application

## Overview
This is a React/Node.js application with PostgreSQL database.

## Architecture
- Frontend: React 18 with TypeScript
- Backend: Node.js with Express  
- Database: PostgreSQL 14

## Current Goals
- [ ] Implement authentication
- [ ] Add API documentation
- [ ] Set up CI/CD pipeline

## Development Guidelines
- Use TypeScript for all new code
- Follow ESLint configuration
- Write tests for new features

Memory Commands

claude /memory           # Edit project memory
claude /memory view      # View current memory

Advanced Thinking

# These "thinking" phrases may work:
claude "think hard about the security implications of this code"
claude "analyze this thoroughly and provide detailed recommendations"

Multi-Directory Workspaces

# Add multiple directories
claude --add-dir ../frontend ../backend ../shared

# Project-wide analysis
claude "analyze the entire application architecture"

---

💡 Best Practices

Effective Prompting

# Good: Specific and detailed
claude "Review UserAuth.js for security vulnerabilities, focusing on JWT handling"

# Bad: Vague  
claude "check my code"

Security Best Practices

1. Start with minimal permissions: claude --allowedTools "View"
2. Use environment variables: export API_KEY="secret"
3. Regular audits: claude config get allowedTools
4. Avoid dangerous mode: Only use --dangerously-skip-permissions in containers

Performance Tips

1. Use appropriate output formats: --output-format json for automation
2. Be specific in prompts: Better results, faster execution
3. Clean up regularly: Remove old sessions and cache

---

Getting Help

• Official Documentation: https://docs.anthropic.com/en/docs/claude-code/overview
• Report Issues: Use /bug command (if it works) or file GitHub issues
• Test First: Always test commands in safe environments before relying on them

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Last Updated: Based on package version 1.0.38 and available documentation. Many features require verification in your specific installation.

Monitoring & Alerting

1. Health Check Automation

# Regular health checks
*/15 * * * * /usr/local/bin/claude /doctor > /dev/null || echo "Claude health check failed" | mail -s "Alert" admin@company.com

2. Log Analysis

# Daily log analysis
0 6 * * * tail -1000 /var/log/app.log | claude -p "analyze for issues" --output-format json > /tmp/daily-analysis.json

Collaboration Best Practices

Team Workflows

1. Shared Configuration Templates

# Create team templates
mkdir -p ~/.claude/templates/
cat > ~/.claude/templates/team-frontend.json << EOF
{
  "allowedTools": ["Edit", "View", "Bash(npm:*)", "mcp__git__*"],
  "model": "claude-sonnet-4",
  "systemPrompt": "You are working on our React frontend. Follow our coding standards and use TypeScript."
}
EOF

# Use templates
claude config import ~/.claude/templates/team-frontend.json

2. Documentation Automation

# Automated documentation updates
claude "update README.md with recent changes to the API endpoints"
claude "generate TypeScript definitions from the new database schema"

3. Code Review Standards

# Standardized review process
claude --allowedTools "View,mcp__git__*" \
  "review PR #123 using our team standards:
  - Security best practices
  - Performance considerations  
  - Code style compliance
  - Test coverage adequacy"

Knowledge Sharing

1. Create Project Runbooks

# Generate runbooks
claude "create a deployment runbook for this application including all steps and troubleshooting"
claude "document the onboarding process for new developers"

2. Architecture Documentation

# Maintain architecture docs
claude "update architecture documentation to reflect recent microservices changes"
claude "create sequence diagrams for the new authentication flow"

Common Pitfalls to Avoid

Security Pitfalls

❌ Don't:

• Use --dangerously-skip-permissions on production systems
• Hardcode secrets in commands or configuration
• Grant overly broad permissions
• Run with elevated privileges unnecessarily

✅ Do:

• Use environment variables for secrets
• Start with minimal permissions
• Regular security audits
• Isolate sensitive operations

Performance Pitfalls

❌ Don't:

• Load entire large codebases unnecessarily
• Use maximum thinking budget for simple tasks
• Run multiple concurrent Claude instances
• Ignore memory and cache cleanup

✅ Do:

• Use focused context with --add-dir
• Match thinking budget to task complexity
• Monitor resource usage
• Clean up regularly

Workflow Pitfalls

❌ Don't:

• Skip project context setup (CLAUDE.md)
• Use vague, ambiguous prompts
• Ignore error messages and logs
• Automate without testing first

✅ Do:

• Maintain comprehensive project context
• Be specific and detailed in requests
• Monitor and analyze logs
• Test automation in safe environments

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