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

Claude Code - Complete Command Reference

The most comprehensive Claude Code command reference available 📚

Discover hidden commands, advanced flags, and power-user techniques that most developers don't know about.

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Table of Contents

• Quick Start
• Core CLI Commands
• CLI Flags & Options
• Configuration Commands
• Slash Commands
• Environment Variables
• Hidden Features
• Advanced Usage
• Output Formats
• Integration Examples
• Troubleshooting
• Configuration Files
• Security
• Beta Features

Quick Start

Essential Commands (Click to expand)

# 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

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Core CLI Commands

Interactive Commands

Command	Description	Example
claude	Start interactive REPL	claude
claude "query"	REPL with initial prompt	claude "help me debug this"
claude -p "query"	One-off query (print mode)	claude -p "explain this function"
cat file | claude -p	Process piped content	cat error.log | claude -p "summarize"

Management Commands

Command	Description	Use Case
claude config	Configure settings	Initial setup
claude update	Update to latest version	Stay current
claude mcp	Configure MCP servers	Add integrations

CLI Flags & Options

Essential Flags

Flag	Short	Description	Example
--print	-p	Print response without interactive mode	claude -p "help"
--resume	-r	Resume specific session by ID	claude -r abc123
--continue	-c	Load most recent conversation	claude -c
--verbose	-	Enable detailed logging	claude --verbose
--debug	-d	Enable debug mode	claude --debug
--help	-h	Show help information	claude --help

Output Format Control

Format Options

Flag	Options	Description
--output-format	text, json, stream-json	Control response format
--input-format	text, stream-json	Control input format
--json	-	Shorthand for JSON output

Examples:

# Text output (default)
claude -p "help" --output-format text

# Structured JSON
claude -p "analyze" --output-format json

# Streaming JSON for real-time
claude -p "process" --output-format stream-json

Permission & Security Flags

⚠️ Warning: Use security flags with extreme caution!

Security Controls

Flag	Risk Level	Description
--dangerously-skip-permissions	HIGH	Skip ALL permission prompts
--allowedTools <tools>	LOW	Whitelist specific tools
--disallowedTools <tools>	LOW	Blacklist specific tools

Safe Examples:

# Allow only git operations
claude --allowedTools "Bash(git:*)"

# Allow file editing only
claude --allowedTools "Edit,View"

# DANGEROUS - skip all checks
claude --dangerously-skip-permissions

Advanced/Hidden Flags

Expert-Level Options

System Control

Flag	Purpose	Example
--mcp-debug	Debug MCP connections	claude --mcp-debug
--max-turns <n>	Limit agentic interactions	claude --max-turns 5
--add-dir <path>	Add working directories	claude --add-dir ../lib ../src
--model <model>	Set specific model	claude --model sonnet

Prompt Engineering

Flag	Purpose	Example
--system-prompt	Override system prompt	claude --system-prompt "You are an expert"
--append-system-prompt	Append to system prompt	claude --append-system-prompt "Focus on security"
-system	Alternative syntax	claude -system "Custom prompt"

Tool Management

Flag	Purpose	Example
--permission-prompt-tool	Custom permission handler	claude --permission-prompt-tool auth_tool
--allow-tool	Allow specific tool	claude --allow-tool Edit
--disallow-tool	Block specific tool	claude --disallow-tool Bash

Experimental Flags

Under Development: These flags are proposed/experimental

Future Features

Flag	Status	Purpose
--no-memory	Proposed	Disable CLAUDE.md loading
--no-tools	Proposed	Exclude tool context
--no-env	Proposed	Disable environment context

Cloud Provider Integration

Provider	Flag	Service
Amazon Bedrock	--use-bedrock	AWS
Google Vertex AI	--use-vertex	GCP

# Use AWS Bedrock
claude --use-bedrock "analyze this code"

# Use Google Vertex AI
claude --use-vertex "help with deployment"

Configuration Commands

Config Management

Command	Purpose	Scope	Example
claude config list	List all settings	Current	claude config list
claude config get <key>	Get specific value	Current	claude config get model
claude config set <key> <value>	Set value	Project	claude config set model sonnet
claude config set -g <key> <value>	Set global value	Global	claude config set -g model opus
claude config add <key> <value>	Add to list	Current	claude config add allowedTools Edit
claude config remove <key> <value>	Remove from list	Current	claude config remove allowedTools Bash

Quick Setup:

# Set global preferences
claude config set -g model claude-sonnet-4
claude config set -g verbose true

# Set project-specific settings
claude config set allowedTools "Edit,View,Bash(git:*)"

MCP Commands

MCP: Model Context Protocol for extending Claude's capabilities

MCP Server Management

Command	Purpose	Example
claude mcp serve	Start MCP server	claude mcp serve
claude mcp add <name> <cmd>	Add stdio server	claude mcp add git "git-mcp-server"
claude mcp remove <name>	Remove server	claude mcp remove git

Popular MCP Servers:

# Database integration
claude mcp add postgres "postgres-mcp-server"

# Web browsing
claude mcp add browser "browser-mcp-server"

# File system operations
claude mcp add fs "filesystem-mcp-server"

Slash Commands

Interactive Mode Only: These commands work inside the Claude REPL

Core Slash Commands

Essential Commands

Command	Purpose	Quick Tip
/help	Show all commands	Start here!
/clear	Clear conversation	Fresh start
/status	System information	Check everything
/cost	Token usage stats	Monitor spending
/exit	Exit safely	Clean shutdown

Management Commands

Command	Purpose	When to Use
/config	View/modify settings	Setup & tuning
/permissions	Manage tool access	Security control
/doctor	Health check	Troubleshooting
/init	Create CLAUDE.md	New projects
/bug	Report issues	Found a problem?

History & Session Commands

Command	Purpose	Pro Tip
/undo	Revert last change	Instant rollback
/compact	Compress conversation	Save context
/login	Switch accounts	Multi-account
/logout	Sign out	Security

Interface Commands

Command	Purpose	For Users Who
/vim	Enable Vim keybindings	Love Vim

Advanced Slash Commands

Workspace Management

Command	Purpose	Example
/add-dir <path>	Add working directory	/add-dir ../backend
/memory	Edit memory files	/memory
/model <name>	Change AI model	/model claude-opus-4

Integration Commands

Command	Integration	Purpose
/ide	IDE Tools	Manage IDE integrations
/mcp	MCP Servers	Manage MCP connections
/install-github-app	GitHub	Setup GitHub Actions
/pr-comments	GitHub	Get PR comments
/review	GitHub	Review pull requests

AI Enhancement Commands

Command	Purpose	Level
/think	Extended thinking mode	Advanced
/upgrade	Access Claude Max	Premium
/user	Personal commands	Custom

Experimental Commands

Command	Status	Purpose
/terminal-setup	Proposed	Terminal optimizations

Custom Slash Commands

Build Your Own: Create custom commands for repeated workflows

Type	Pattern	Storage Location	Scope
Project	/project:<command>	.claude/commands/	Current project
Personal	/user:<command>	~/.claude/commands/	All projects

Examples:

# Project-specific workflow
/project:deploy     # Deploy this project
/project:test-all   # Run full test suite

# Personal shortcuts
/user:morning       # Daily startup routine
/user:review-pr     # PR review checklist

Environment Variables

Core Configuration Variables

Variable	Purpose	Example	Required
ANTHROPIC_API_KEY	API Authentication	sk-ant-api03-xxx	Yes
ANTHROPIC_MODEL	Default model	claude-sonnet-4	No
ANTHROPIC_SMALL_FAST_MODEL	Quick operations	claude-haiku-3	No

Quick Setup:

# Essential - Add to your ~/.bashrc or ~/.zshrc
export ANTHROPIC_API_KEY="sk-ant-api03-your-key-here"

# Optional - Set default model
export ANTHROPIC_MODEL="claude-sonnet-4"

Claude Code Specific Variables

Cloud Provider Integration

Variable	Cloud	Purpose
CLAUDE_CODE_USE_BEDROCK	AWS	Enable Bedrock integration
CLAUDE_CODE_USE_VERTEX	GCP	Enable Vertex AI integration
CLAUDE_CODE_SKIP_BEDROCK_AUTH	AWS	Skip authentication (gateways)
CLAUDE_CODE_SKIP_VERTEX_AUTH	GCP	Skip authentication (gateways)

Telemetry & Privacy

Variable	Purpose	Privacy Impact
CLAUDE_CODE_DISABLE_NONESSENTIAL_TRAFFIC	Disable all non-essential traffic	High Privacy
CLAUDE_CODE_ENABLE_TELEMETRY	Control telemetry	Configurable

Privacy-First Setup:

# Maximum privacy
export CLAUDE_CODE_DISABLE_NONESSENTIAL_TRAFFIC=1

Feature Control Variables

Privacy & Security Controls

Variable	Feature	Privacy Level
DISABLE_AUTOUPDATER=1	Auto-updates	Medium
DISABLE_BUG_COMMAND=1	Bug reporting	High
DISABLE_ERROR_REPORTING=1	Error reports	High
DISABLE_TELEMETRY=1	Analytics	High

Cost & Performance Controls

Variable	Feature	Cost Impact
DISABLE_COST_WARNINGS=1	Cost alerts	None
DISABLE_NON_ESSENTIAL_MODEL_CALLS=1	Extra AI calls	Saves Money
DISABLE_PROMPT_CACHING=1	Caching	Costs More

Recommended Privacy Setup:

# Privacy-focused configuration
export DISABLE_TELEMETRY=1
export DISABLE_ERROR_REPORTING=1
export DISABLE_BUG_COMMAND=1

# Cost optimization
export DISABLE_NON_ESSENTIAL_MODEL_CALLS=1

Network & Proxy Variables

Variable	Protocol	Example
HTTP_PROXY	HTTP	http://proxy.company.com:8080
HTTPS_PROXY	HTTPS	https://proxy.company.com:8443

Corporate Network Setup:

# Corporate proxy configuration
export HTTP_PROXY="http://proxy.company.com:8080"
export HTTPS_PROXY="https://proxy.company.com:8443"

Advanced Configuration Variables

AI Behavior Tuning

Variable	Purpose	Example
MAX_THINKING_TOKENS	Thinking budget	MAX_THINKING_TOKENS=50000
MCP_TIMEOUT	MCP startup timeout	MCP_TIMEOUT=10000

Regional Configuration

Variable	Cloud Provider	Purpose
AWS_REGION	AWS Bedrock	us-east-1
CLAUDE_ML_REGION	GCP Vertex	us-central1

Multi-Region Setup:

# AWS Bedrock in US East
export AWS_REGION="us-east-1"

# GCP Vertex in US Central
export CLAUDE_ML_REGION="us-central1"

Recent Updates (2025)

Version 1.0.25 (Latest)

New Features

• Fixed slash command reliability issues
• Improved /mcp output functionality
• Fixed settings array merge bug

June 18, 2025 Update

• SSE Transport: Real-time MCP communication
• HTTP Transport: Web-based MCP servers
• Remote MCP: Cloud MCP functionality
• Enhanced Auth: Better MCP authentication

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Hidden Features

Secret Sauce: Features most users don't know about

Tool Permission Patterns

Precise Tool Control

Allowlist Patterns

Pattern	Scope	Example
"Tool"	Entire tool	"Edit"
"Tool(scope:*)"	Scoped access	"Bash(git:*)"
"Tool1,Tool2"	Multiple tools	"Edit,View"
"mcp__server__tool"	MCP tools	"mcp__puppeteer__navigate"

Common Patterns

# Text editing only
claude --allowedTools "Edit,View"

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

# Development workflow
claude --allowedTools "Edit,View,Bash(npm:*),Bash(git:*)"

# Web automation
claude --allowedTools "mcp__puppeteer__puppeteer_navigate,mcp__puppeteer__puppeteer_click"

Advanced Usage

Automation Patterns

Headless Automation

# JSON output for scripts
claude -p "analyze code" --output-format stream-json

# Dangerous mode (containerized only!)
claude --resume abc123 --dangerously-skip-permissions

# Debug everything
claude --verbose --mcp-debug

AI Behavior Control

Prompt Engineering

# Custom system prompt
claude --system-prompt "You are a security expert" -p "review code"

# Append to system prompt
claude --append-system-prompt "Focus on vulnerabilities" -p "review"

# Thinking levels
claude "think about this"           # Basic (1K tokens)
claude "think hard about this"      # Enhanced
claude "ultrathink about this"      # Maximum (128K tokens)

Interactive Mode Tricks

Keyboard Shortcuts

Shortcut	Mode	Purpose
Shift+Tab (1x)	Auto-Accept	Skip confirmations
Shift+Tab (2x)	Planning	Analyze without writing
Escape	Interrupt	Stop Claude anytime
Escape (2x)	History	Edit previous prompts

Workflow Example:

1. Start Claude Code
2. Press Shift+Tab twice → Planning mode
3. Describe task → Claude plans without executing
4. Review plan → Exit planning mode to execute

Advanced Configurations

Power User Setup

# Multi-directory workspace
claude --add-dir ../apps ../lib ../shared

# Controlled execution
claude -p --max-turns 3 "refactor function"

# Custom permission handler
claude -p --permission-prompt-tool mcp_auth_tool "write files"

# Specific model selection
claude --model claude-sonnet-4-20250514 "analyze codebase"

# Extended thinking + tools (beta)
claude "ultrathink about this migration and use tools as needed"

Power User Aliases

Community Shortcuts

⚠️ Warning: Use dangerous aliases only in safe environments!

# Quick access (add to ~/.bashrc or ~/.zshrc)
alias cc="claude --dangerously-skip-permissions"  # DANGEROUS
alias yolo="claude --dangerously-skip-permissions" # VERY DANGEROUS

# Output formats
alias claude-json="claude -p --output-format json"
alias claude-stream="claude -p --output-format stream-json"

# Safe shortcuts
alias cl="claude"                                   # Simple shortcut
alias clp="claude -p"                              # Print mode
alias cls="claude /status"                         # Quick status

Configuration Files

Settings Files

File	Scope	Purpose
~/.claude.json	Global	User-wide settings
.claude/settings.json	Project	Project-specific config
~/.config/claude-code/auth.json	Auth	Authentication data

Custom Commands

Directory	Scope	Command Pattern
.claude/commands/	Project	/project:command
~/.claude/commands/	Personal	/user:command

MCP Configuration

File	Purpose
.claude/mcp.json	MCP server config
~/.claude-code-mcp.env	MCP environment vars

Security

Dangerous Flags

⚠️ EXTREME CAUTION REQUIRED

Flag	Risk Level	Impact
--dangerously-skip-permissions	CRITICAL	Bypasses ALL security checks

Safe Usage Guidelines:

• Only use in containerized environments
• Never use with internet access
• Can cause data loss/corruption
• Major security vulnerability

Safe Usage Patterns

Security Best Practices

Always Review First

• Review commands before granting permissions
• Use /permissions to audit settings
• Use /doctor for security health checks

Principle of Least Privilege

• Avoid blanket permissions
• Use specific tool allowlists
• Regular permission audits

Security Commands

# Check security status
claude /doctor

# Review permissions
claude /permissions

# Safe tool allowlist
claude --allowedTools "Edit,View"

Output Formats

Text Output (Default)

# Standard human-readable output
claude -p "explain this function" --output-format text

Example Output

This function calculates the factorial of a number recursively...

JSON Output

# Structured data with metadata
claude -p "analyze this code" --output-format json

Example Output

{
  "response": "This function calculates...",
  "metadata": {
    "cost": 0.0023,
    "duration": 1.2,
    "model": "claude-sonnet-4"
  }
}

Streaming JSON Output

# Real-time streaming for large operations
claude -p "process large file" --output-format stream-json

Example Output

{"type": "start", "timestamp": "2025-06-23T10:00:00Z"}
{"type": "progress", "content": "Processing..."}
{"type": "result", "content": "Analysis complete"}
{"type": "end", "timestamp": "2025-06-23T10:00:05Z"}

⚠️ Note: Each line is valid JSON, but concatenated output is not valid JSON

Integration Examples

CI/CD Integration

Build Pipeline Examples

# Automated fixing in build scripts
claude -p "fix linting errors" --dangerously-skip-permissions --output-format json

# Controlled tool access
claude -p "run tests and fix failures" --allowedTools "Bash(npm:*),Edit"

# Pipeline integration
if claude -p "check code quality" --output-format json | jq -r '.passed'; then
  echo "Quality checks passed"
else
  echo "Quality issues found"
  exit 1
fi

Scripting Integration

Automation Scripts

# Log analysis
cat error.log | claude -p "summarize errors" --output-format json > summary.json

# Batch processing
for file in *.py; do
    claude -p "review this Python file" < "$file" --output-format text >> review.txt
done

# Monitoring integration
journal_errors=$(journalctl --since "1 hour ago" --priority=err)
echo "$journal_errors" | claude -p "analyze system errors" --output-format json > /tmp/error_analysis.json

Troubleshooting

Health Checks

Command	Purpose	When to Use
claude --help	📚 Show all options	Getting started
/doctor	🩺 Health check	Something's wrong
/status	📊 Current config	Check settings
claude config list	📝 List all settings	Audit configuration

Debug Mode

Debug Commands

# Detailed logging
claude --verbose

# Full debug mode
claude --debug

# MCP-specific debugging
claude --mcp-debug

# Combined debugging
claude --verbose --debug --mcp-debug

Reset & Recovery

Emergency Recovery

# Reset authentication
rm -rf ~/.config/claude-code/auth.json

# Clean logout/login
claude /logout
claude /login

# Reset all settings
rm -rf ~/.claude.json
rm -rf .claude/settings.json

# Full health check after reset
claude /doctor

Beta Features

Interactive Mode Controls

Shortcut	Action	Mode
Shift+Tab (1x)	Auto-Accept	Skip confirmations
Shift+Tab (2x)	Planning	Analyze without writing
Escape	Interrupt	Stop Claude anytime
Escape (2x)	History	Edit previous prompts

Thinking Budget Control

Secret: Special phrases control AI thinking depth

Thinking Levels

Phrase	Thinking Budget	Use Case
"think"	1,024 tokens	Basic analysis
"think hard"	Enhanced	Complex problems
"think harder"	Advanced	Deep analysis
"think more"	Alternative enhanced	Thorough review
"ultrathink"	128K tokens	Maximum depth
"megathink"	Alternative max	Alternative maximum

Examples:

# Basic thinking
claude "think about this algorithm"

# Enhanced thinking
claude "think hard about the security implications"

# Maximum thinking
claude "ultrathink about this database migration"

Extended Thinking Mode

Advanced Thinking Controls

# Slash command trigger
/think

# Custom budget (proposed)
--thinking-budget 50000

Permission Prompt Tool Integration

Custom Permission Handler

The --permission-prompt-tool expects an MCP tool that returns JSON:

Allow Execution

{
  "behavior": "allow",
  "updatedInput": {...}  // original or modified input
}

Deny Execution

{
  "behavior": "deny",
  "message": "Reason for denial"
}

GitHub Integration Features

Feature	Status	Description
@claude mentions	Beta	PR/Issue mentions
GitHub Actions	Beta	Automated workflows
gh CLI integration	Stable	Repository operations
IDE extensions	Beta	VS Code & JetBrains
Inline edits	Beta	IDE interface edits

Experimental Features

Cutting-Edge Capabilities

AI Enhancements

• Extended thinking with tool use: Claude uses tools during thinking
• Parallel tool execution: Multiple tools run simultaneously
• 128K output tokens: 15x longer responses

Interactive Modes

• Planning mode: Shift+Tab twice for analysis without writes
• Auto-accept mode: Shift+Tab once for autonomous implementation

Integrations

• IDE integrations: VS Code and JetBrains extensions
• Advanced memory system: Multi-tiered contextual memory

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Important Notes

Command Precedence & Behavior

Command Precedence

Query > Session > App Config > Environment Variables > Defaults

Key Behaviors

1. Session Management: Each command can specify session name for isolation
2. Tool Names: Use exact names like "Replace", "Edit", "Bash", "View"
3. MCP Integration: Model Context Protocol with SSE/HTTP support
4. Version Updates: Use claude update for latest features
5. DMCA Notice: Decompiled source repository was taken down
6. Beta Features: GitHub Actions, IDE extensions in beta
7. Thinking Modes: Special phrases trigger different thinking levels
8. Latest Version: 1.0.25 (June 2025) with improved reliability
9. Real-time Features: SSE transport enables real-time MCP communication

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✅ Research Verification

COMPLETE RESEARCH CONDUCTED

Source	Status
Official Documentation	Thoroughly Reviewed
GitHub Repository & Issues	Comprehensively Analyzed
Community Discussions	Extensively Searched
CLI Reference	Completely Documented
Environment Variables	Fully Catalogued
Slash Commands	Entirely Mapped
Hidden Features	Discovered & Documented
2025 Updates	Latest Changelog Reviewed
Source Code Analysis	Completed (pre-DMCA)

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The Most Complete Claude Code Reference

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