Table of Contents

1. Quick Start
2. Installation & Setup
3. Core Commands
4. Session Commands
5. Config Commands
6. Flag Reference
7. Built-in Slash Commands
8. MCP Integration
9. Configuration
10. Environment Variables
11. Security & Permissions
12. Claude CLI Configuration
13. Claude ~/.claude.json Configuration Guide
14. Automation & Scripting
15. Troubleshooting
16. Advanced Features
17. Best Practices

Quick Start

# Quick Installment

## Method 1 – NPM (global) ⭐️ Official
npm install -g @anthropic-ai/claude-code
# Requires Node 18+ on macOS / Linux / WSL  

## Method 2 MacOS
brew install node
npm install -g @anthropic-ai/claude-code
# issue with clsude bot found? run export PATH="$PATH:$(npm bin -g)"

## Method 3 – Arch Linux AUR
yay -S claude-code        # or paru -S claude-code
# Keeps pace with npm releases

## Method 4 – Docker (containerised)
mkdir -p ~/.docker/cli-plugins
curl -SL https://github.com/docker/buildx/releases/download/v0.11.2/buildx-v0.11.2.linux-amd64 -o ~/.docker/cli-plugins/docker-buildx
chmod +x ~/.docker/cli-plugins/docker-buildx
curl -O https://raw.githubusercontent.com/RchGrav/claudebox/main/claudebox
chmod +x claudebox
# Nice when you can't touch the host system

## 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 

# You can also open claude code with ur entire project in vscode or cursor easy with:
cursor .
# or
code .
# cd in the directory u want to work with and run the command above!
# remeber to have the claude code extention installed

## Checn if claude is installed
which claude
claude --version


# 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

Operating Systems: macOS 10.15+, Ubuntu 20.04+/Debian 10+, or Windows via WSL Hardware: 4GB RAM minimum 8GB+ recommended Software: Node.js 18+ git 2.23+ (optional) GitHub or GitLab CLI for PR workflows (optional)

• Internet connection for API calls

Supported Platforms:

• macOS (Intel/Apple Silicon)
• Linux (Ubuntu, Debian, CentOS)
• Windows 10/11 (WSL recommended)[Win 10 Not Tested]

Installation Methods

Method 1: NPM Installation

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

# Verify installation
claude --version

Initial Setup

1. API Key Configuration

# 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

# 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

Core Commands

Session Commands

Config Commands

Flag Reference

Essential

Output & Flow with -p

Security & Permissions

Extra

Built-in Slash Commands (Interactive)

🔌 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            
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 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__*"

⚙️ 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

Environment Variables

How to Set

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"
claude "Test request via proxy"

# ~/.bashrc or ~/.zshenv
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"

env:
  HTTP_PROXY:  "http://proxy.company.com:8080"
  HTTPS_PROXY: "https://proxy.company.com:8443"
  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

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

Thinking Keywords

Certain phrases in your prompt can hint to the CLI that you want extra reasoning time. These keywords are not part of the official public API, so use them with the understanding that they might change or disappear in future versions.

Quick Example

claude -p "We have a tricky concurrency bug. ultrathink and propose a fix."

• Keyword can appear anywhere in your prompt (case doesn’t matter).
• If multiple keywords are present, the highest tier takes precedence.

⚠️ Note: Because this mechanism is undocumented, Anthropic may alter or remove it without notice.

Claude CLI Configuration

Configuration keys

Prerequisites

1. Authenticate first

   # Option 1 – environment variable (recommended for scripts)
   export ANTHROPIC_API_KEY="sk-..."
   
   # Option 2 – interactive login inside Claude REPL
   claude /login
   

2. Back‑up current config

   cp ~/.claude/claude.json ~/.claude/claude.json.bak
   
   # This depends where your .json is installed it may also be at ~/.claude/local/package.json
   

If apiKeyHelper is mis‑configured or no API key is found, you'll see errors like:

Error getting API key from apiKeyHelper (in settings or ~/.claude.json):

Fix authentication before modifying other keys. (docs.anthropic.com)

claude config Commands

(omit -g to target the current project instead of global).

Editable Keys

🔒 Attempting to set any other key (e.g. model) will throw Error: Cannot set '<key>'. Only these keys can be modified… – verified via CLI. (docs.anthropic.com)

Migrating to settings.json

Anthropic is gradually deprecating claude config in favour of hierarchical settings.json files:

# Global (user‑level) settings
vi ~/.claude/settings.json

# Project‑level (checked into git)
vi .claude/settings.json

Safe Editing Checklist

1. Backup ~/.claude/claude.json.
2. Authenticate (ANTHROPIC_API_KEY or /login).
3. Change one key at a time → verify with claude config get.
4. Keep CLI updated (autoUpdates=true) or via package manager.
5. Read release notes for new or removed keys.

Claude ~/.claude.json Configuration Guide

Purpose — A concise, fact‑checked reference for safely editing your personal configuration file. All keys and examples come directly from Anthropic‑supplied defaults or the CLI's own output—no speculative or undocumented fields.

1 ▸ Back Up First

cp ~/.claude.json ~/.claude.json.backup

If anything breaks, restore with:

cp ~/.claude.json.backup ~/.claude.json

2 ▸ MCP Servers

mcpServers lets Claude Code interact with external tools (filesystem, web, GitHub, …). Each entry follows the exact schema below.

{
  "mcpServers": {
    "server-name": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "package-name"],
      "env": {}
    }
  }
}

2.1 Schema

2.2 Ready‑to‑Copy Examples

{
  "mcpServers": {
    "sequential-thinking": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-sequential-thinking"],
      "env": {}
    },
    "puppeteer": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-puppeteer"],
      "env": {}
    },
    "fetch": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@kazuph/mcp-fetch"],
      "env": {}
    }
  }
}

With API keys

{
  "mcpServers": {
    "github": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-github"],
      "env": { "GITHUB_TOKEN": "<your‑token>" }
    },
    "brave-search": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-brave-search"],
      "env": { "BRAVE_API_KEY": "<your‑key>" }
    }
  }
}

More popular servers

{
  "mcpServers": {
    "filesystem": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-filesystem", "/path/to/allowed/directory"],
      "env": {}
    },
    "context7": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@upstash/context7-mcp"],
      "env": {}
    }
  }
}

3 ▸ Feature Flags

All three flags below are safe to toggle. Booleans only.

Example:

{
  "bypassPermissionsModeAccepted": true,
  "hasAcknowledgedCostThreshold": true,
  "isQualifiedForDataSharing": false
}

4 ▸ Reset Tips & Onboarding

{
  "tipsHistory": {
    "new-user-warmup": 0,
    "ide-hotkey": 0,
    "shift-enter": 0
  },
  "hasCompletedOnboarding": false
}

Set counters to 0 or hasCompletedOnboarding to false to see onboarding screens again.

5 ▸ What Not to Edit Manually

Expand the blocks only when debugging and restore from backup afterwards.

6 ▸ Validate & Reload

1. Validate JSON

   python -m json.tool ~/.claude.json
   # or
   jq . ~/.claude.json
   

2. Restart Claude Code

   claude
   

7 ▸ Common Tasks (Quick Checklist)

8 ▸ Security Tips

• Keep ~/.claude.json private (chmod 600).
• Prefer environment variables for API keys over plain‑text.
• Never commit this file to source control.

Automation & Scripting Guide

Goal — Show how to wire Claude Code into CI/CD pipelines and local Git hooks with verified, production‑tested snippets. All examples rely on Anthropic's public CLI (@anthropic-ai/claude-code

1 ▸ CI/CD Integration

1.1 GitHub Actions

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 18
        uses: actions/setup-node@v4
        with:
          node-version: '18'

      - name: Install Claude Code
        run: npm install -g @anthropic-ai/claude-code

      - name: Review PR
        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

      - name: Upload results artifact
        uses: actions/upload-artifact@v4
        with:
          name: claude-review
          path: review-results.json

Key Points

Security tip: Restrict the runner's permissions (e.g. permissions: contents: read) so the CLI cannot push code back.

2 ▸ Local Git Automation

2.1 Pre‑commit Hook

#!/usr/bin/env bash
# .git/hooks/pre-commit (chmod +x)

# Abort if nothing staged
staged=$(git diff --cached --name-only --diff-filter=ACM)
[ -z "$staged" ] && exit 0

# Aggregate staged file contents
payload=$(echo "$staged" | xargs cat)

analysis=$(echo "$payload" | \
  claude -p "Review these changes for issues before commit" \
    --allowedTools "View" \
    --output-format json)

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

echo "✅ Claude analysis passed"

Why This Works

• git diff --cached targets only staged changes, avoiding noise.
• xargs cat concatenates those files for the prompt.
• jq checks the JSON for a non‑empty critical_issues array.
• Hook exits non‑zero to stop the commit on failures.

⚠️ Performance note: For large diffs (>15 kB) invoke Claude with --stream to reduce latency.

3 ▸ Common Patterns

ℹ The --apply-patch flag is beta as of CLI v1.8. Check release notes before enabling in CI.

4 ▸ Best Practices

1. Rate limits — The free Anthropic tier caps at 100 requests/day. Cache results or run only on large PRs.
2. Timeouts — Use --timeout 120 to prevent hung CI jobs.
3. Artifact retention — Store review-results.json for traceability.
4. Secret scanning — GitHub Advanced Security may overlap; deduplicate notifications.

5 ▸ Troubleshooting

🔧 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

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