Jatin Bansal
Tools· · 6 min read

Claude Code Commands Reference

Jatin Bansal

A comprehensive guide to essential Claude Code CLI commands for efficient AI-powered development workflows, with special focus on Docker MCP Gateway integration.

Docker MCP Gateway Management

I prefer to use MCP servers through the Docker MCP Gateway. It provides a unified way for managing MCP servers across different tools like Cursor, Claude, and other AI clients without manual configuration for each tool.

Key Benefits:

  • Centralized MCP server management
  • Container-based isolation and security
  • Unified configuration across clients
  • Built-in secret management
  • Server catalog discovery

Learn more: Docker MCP Gateway: Open Source, Secure Infrastructure for Agentic AI ↗

Docker MCP Gateway Configuration

Basic Gateway Configuration (Claude Desktop)

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{
  "globalShortcut": "Alt+Space",
  "mcpServers": {
    "DOCKER": {
      "command": "env",
      "args": [
        "PATH=/Applications/Docker.app/Contents/Resources/bin:/usr/local/bin:/opt/homebrew/bin:/usr/bin:/bin:/usr/sbin:/sbin",
        "/Applications/Docker.app/Contents/Resources/bin/docker",
        "mcp",
        "gateway",
        "run"
      ]
    }
  }
}

Advanced Gateway Configuration

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# Run gateway with security features enabled
docker mcp gateway run \
  --verify-signatures \
  --log-calls \
  --block-secrets

# Run gateway with specific servers and transport
docker mcp gateway run \
  --transport=sse \
  --servers=wikipedia-mcp \
  --tools=get_article,get_summary,get_related_topics

# Servers I have currently enabled  
docker mcp server list
# context7, docker, duckduckgo, fetch, filesystem, sequentialthinking, time

Server Catalog Management

bash 
# View available MCP servers in catalog
docker mcp catalog show

# Enable specific servers
docker mcp server enable google-maps brave

# Disable servers
docker mcp server disable <server-name>

Secret and Configuration Management

bash 
# Set API keys and secrets
docker mcp secret set 'brave.api_key=YOUR_API_KEY'
docker mcp secret set 'github.token=YOUR_GITHUB_TOKEN'

# View current configuration
docker mcp config read

Gateway Security Features

  • Container Isolation: Each MCP server runs in isolated Docker containers
  • Signature Verification: Verify provenance of MCP container images
  • Secret Scanning: Block secrets in inbound/outbound payloads
  • Network Restrictions: Controlled network access for servers
  • Resource Limits: CPU and memory constraints per server

Traditional MCP Server Management

List MCP Servers

shell 
claude mcp list

Purpose: Display all configured MCP (Model Context Protocol) servers and their status.

Add MCP Servers from Claude Desktop

shell 
claude mcp add-from-claude-desktop -s user

Purpose: Import MCP server configurations from Claude Desktop application to Claude Code CLI.

Remove MCP Server

shell 
claude mcp remove <server-name> -s user

Purpose: Remove an MCP server configuration.

Add MCP Servers (Manual Configuration)

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# Add stdio server
claude mcp add <server-name> <command> [args...]

# Add SSE server
claude mcp add --transport sse <server-name> <url>

# Add HTTP server
claude mcp add --transport http <server-name> <url>

# Add with specific scope
claude mcp add --scope user <server-name> <command>
claude mcp add --scope project <server-name> <command>

Get Server Details

bash 
claude mcp get <server-name>

Purpose: Display detailed information about a specific MCP server configuration.

Output Formats & Scripting

JSON Output for Automation

bash 
# Get structured JSON response
claude -p "analyze this code" --output-format json

# Stream JSON for real-time processing
claude "process large dataset" --output-format stream-json

# Combine with jq for parsing
claude -p "list project dependencies" --output-format json | jq '.content'

Scripting Examples

bash 
# Automated code review
claude -p "review changes in $(git diff --name-only)" > review.md
git diff | claude "review these changes" -p

Configuration & Settings

View Settings File

shell 
cat ~/.claude/settings.json

response:

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{
  "permissions": {
    "allow": [
      "mcp__DOCKER__get-library-docs",
      "mcp__DOCKER__resolve-library-id",
      "mcp__DOCKER__sequentialthinking",
      "mcp__DOCKER__fetch",
      "mcp__DOCKER__search",
      "WebFetch(domain:docs.anthropic.com)",
      "WebFetch(domain:*)",
      "Bash(npm run lint)",
      "mcp__DOCKER__fetch_content",
      "mcp__DOCKER__list_directory",
      "mcp__DOCKER__read_multiple_files",
      "mcp__DOCKER__read_file"
    ],
    "deny": []
  }
}

Purpose: Display current Claude Code configuration including MCP servers, shortcuts, and allowed tools. I use this configuration to auto allow of these tools

Session Management

Start Interactive Session

shell 
claude chat

Purpose: Begin a new interactive conversation with Claude.

Resume Previous Session

shell 
claude --resume
# or
claude -c

Purpose: Continue from your last conversation session.

Enhanced Development Workflow

Model Selection & Performance

shell 
# Use specific model
claude --model claude-3-7-sonnet-latest
claude --model claude-3-5-sonnet-20241022
claude --model claude-3-5-haiku-20241022

# Model comparison workflow
claude --model claude-3-5-sonnet-20241022 "complex analysis task"
claude --model claude-3-5-haiku-20241022 "simple quick task"

Advanced Command Execution

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# Single command with print flag
claude "your prompt here" -p
claude "your prompt here" --print

# Continue conversation from command
claude -c "follow up question"

# Verbose execution for debugging
claude --debug "debug this issue"

File and Directory Operations

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# Add multiple directories to context
claude --add-dir /path/to/src --add-dir /path/to/tests

# Process file input
claude < analysis-prompt.txt

# Save formatted output
claude "generate report" -p --output-format json > report.json

# Pipe operations
git diff | claude "review these changes" -p

Troubleshooting & Debug

Get Help

shell 
claude --help

Purpose: Display available commands and options.

Show Version

shell 
claude --version

Purpose: Display Claude Code version information.

Debug Mode

shell 
claude --debug

Purpose: Run with detailed debugging information.

Advanced MCP Server Management

Project-Level Configuration

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# Create project-specific MCP configuration
echo '{
  "mcpServers": {
    "project-tools": {
      "command": "npm",
      "args": ["run", "mcp-server"],
      "scope": "project"
    }
  }
}' > .mcp.json

# Use project configuration
claude --mcp-config .mcp.json chat

Multi-Server Workflows

bash 
# Enable multiple complementary servers
claude mcp add filesystem-server file-tools
claude mcp add database-server db-tools  
claude mcp add api-server http-client

Advanced Usage & Integrations

Useful Alias

bash 
# Terminal integration
alias c='claude -p'
alias cr='claude --resume'

Background Processing

shell 
# Run long tasks in background
claude "analyze large codebase" &
# output:- [1] pid
ps pid

Performance Optimization

bash 
# Use faster model for simple tasks
claude --model claude-3-5-haiku-20241022 "quick syntax check"

# Cache frequently used prompts
echo "Review code for security vulnerabilities" > security-review.prompt
claude < security-review.prompt

Debug MCP Issues

shell 
claude --debug mcp list

Troubleshooting & Performance Tips

Common Issues & Solutions

MCP Server Connection Problems

bash 
# Check server status
claude mcp list --debug

Performance Optimization Tips

  1. Choose Right Model: Use Haiku for simple tasks, Sonnet for complex analysis
  2. Cache Prompts: Save frequently used prompts to files
  3. Batch Operations: Group related tasks together
  4. Clean Sessions: Regularly remove old conversation history

Resources & References

Official Documentation

Community Resources

Quick Command Reference

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# Essential commands
claude --help                    # Get help
claude chat                      # Start interactive session
claude -p "query"               # One-time query
claude --resume                 # Resume last session

# MCP management
claude mcp list                 # List servers
claude mcp add <name> <cmd>     # Add server
claude mcp get <name>           # Server details
claude mcp remove <name>        # Remove server

# Docker Gateway
docker mcp gateway run          # Start gateway
docker mcp catalog show         # Browse catalog
docker mcp server enable <name> # Enable server
docker mcp secret set 'key=val' # Set secrets

This comprehensive reference covers Claude Code CLI usage with special focus on Docker MCP Gateway integration. For the latest features and updates, always refer to claude --help or the official documentation ↗.