Claude Code Command Mastery: A Complete Guide to the Three-Layer System

If you have ever opened a terminal and typed claude only to feel overwhelmed by the number of available commands, you are not alone. Claude Code is a powerful assistant for developers, but its command structure can seem chaotic at first glance. The good news is that beneath the surface lies a simple, three-layer system. Once you understand this framework, you will never be confused again.

This guide is based on Claude Code version 2.1.74. While different versions, plans, plugins, and platforms may introduce slight variations, the core principles remain unchanged. Our goal is to give you a clear mental map, the most practical commands, and the confidence to use Claude Code effectively in your daily work.

1. The Three Layers of Claude Code Commands

Claude Code’s command system is built on only three layers. Memorise this structure and you will always know where to look for the right command.

Layer Name What it does Example
First Main command The program entry point you type in your shell claude
Second Subcommands Manage features like authentication, MCP, plugins claude auth login
Third Slash commands Control an active session from inside the REPL /model, /clear

In a nutshell:
The main command opens the program, subcommands manage features, and slash commands control the conversation.

2. Three Main Commands Every Beginner Should Know

These three commands will cover 90% of your interactions with Claude Code. Master them first.

Command Purpose When to use
claude Start an interactive Claude Code session You need a multi‑turn conversation to solve a complex problem
claude -p "task description" Non‑interactive mode: execute once and exit Perfect for scripts, batch processing, or quick one‑off questions
claude -c Continue the most recent session in the current directory Resume an unfinished conversation right where you left off

3. Most Useful Global Parameters (and How to Use Them)

Once you are comfortable with the basic commands, you will want to tailor Claude Code’s behaviour to each task. These parameters are the ones you will reach for most often.

Model and performance

  • --model – Choose which model version to use for this session.
  • --effort – Set the thinking effort level (low, medium, high, max). Use lower effort for simple tasks to save resources.
  • --fallback-model – Specify a backup model for --print mode when the primary model is congested.

Permissions and safety

  • --permission-mode – Define the permission strategy (default, auto, plan, dontAsk).
  • --allowed-tools – Restrict the session to only the listed tools.
  • --disallowed-tools – Explicitly forbid certain tools.
  • --tools – Customise the set of tools available during the session.

Debugging and output

  • --debug – Enable debug mode to see detailed internal information.
  • --debug-file – Write debug logs to a specified file.
  • --verbose – Force verbose output.
  • --output-format – Choose output format (text, json, stream-json).
  • --input-format – Set the input format (usually text or stream-json).

Session and workspace

  • --add-dir – Grant Claude Code access to additional directories beyond the current one. Useful for cross‑directory read/write operations.
  • --session-id – Manually specify a session ID.
  • --fork-session – When resuming an old session, create a forked copy instead of overwriting.
  • --no-session-persistence – Do not save the session to disk.

If you are new to these parameters, start with these five:

  1. --model – Pick the right model for your task.
  2. --effort – Save time and tokens on simple requests.
  3. --permission-mode – Control how often you are asked for tool approval.
  4. --debug – Invaluable when something does not work as expected.
  5. --output-format – Use json when you need structured output for further processing.

4. Parameters That Deserve Extra Caution

The following parameters directly change Claude Code’s behaviour and its safety boundaries. Use them only when you fully understand their implications.

Parameter What it does Why be careful
--dangerously-skip-permissions Bypass all permission prompts The AI can execute potentially system‑altering actions without asking you.
--allow-dangerously-skip-permissions Permit skipping permissions Effectively gives the AI broader autonomy.
--tools Customise the available tool set You might inadvertently enable or disable critical tools.
--system-prompt Override the default system prompt Changes the AI’s fundamental behaviour; can lead to unexpected results.
--permission-mode Switch permission strategies Affects what the AI can do and when it needs your consent.

These parameters are powerful in the right hands, but always double‑check your settings before using them in production or with sensitive projects.

5. Subcommands: Managing Claude Code from the Terminal

Beyond the main command, claude can be followed by various subcommands to configure and maintain the tool. Here are the most common ones:

claude agents        # List or manage agents
claude auth          # Manage login status and account authentication
claude auto-mode     # View auto‑mode classifier configuration
claude doctor        # Check installation health and updater status
claude install       # Install the native version of Claude Code
claude mcp           # Manage MCP servers
claude plugin        # Manage plugins (also works as "plugins")
claude setup-token   # Set a long‑lived authentication token
claude update        # Check for and install new versions (also "upgrade")

5.1 Authentication Commands

These are the first subcommands you will need when setting up Claude Code.

Login and logout

  • claude auth login – Log in to your Anthropic account.
  • claude auth login --email your@email.com – Pre‑fill your email address.
  • claude auth login --sso – Force Single Sign‑On (SSO) login.
  • claude auth logout – Sign out of the current account.

Check authentication status

  • claude auth status – Show human‑readable status.
  • claude auth status --json – Output detailed status in JSON format.

5.2 Auto‑Mode Commands

These commands help you understand how automatic mode selection works. They are especially useful when troubleshooting unexpected behaviour.

  • claude auto-mode config – Display the currently active auto‑mode configuration.
  • claude auto-mode defaults – Show the default auto‑mode rules.

5.3 Doctor, Install, Update, and Setup‑Token

Keep your Claude Code installation healthy with these commands.

Diagnostics

  • claude doctor – Run a health check on the installation and the automatic updater.

Installation and version management

  • claude install stable – Install the latest stable version.
  • claude install latest – Install the most recent build (may be less stable).
  • claude install 1.2.3 – Install a specific version.
  • claude install --force – Force reinstallation even if the version is already present.

Updates and tokens

  • claude update / claude upgrade – Check for and install new versions.
  • claude setup-token – Configure a long‑lived token for automated environments (like CI/CD pipelines).

5.4 MCP Commands in Depth

MCP stands for Model Context Protocol. Think of it as a bridge that lets Claude Code connect to external tools, services, and additional context. Through MCP, you can extend what Claude Code can do.

Basic MCP commands

Command Description
claude mcp list List all configured MCP servers
claude mcp get <name> Show detailed information about a specific MCP
claude mcp add <name> <command_or_url> Add a new MCP server
claude mcp add-json <name> <json> Add an MCP using a JSON configuration
claude mcp add-from-claude-desktop Import MCP settings from Claude Desktop
claude mcp remove <name> Delete an MCP server
claude mcp reset-project-choices Reset approval/denial records for MCPs in the current project
claude mcp serve Start Claude Code’s own MCP server

Common parameters for claude mcp add

Parameter Purpose
--transport Specify transport (stdio, sse, http)
--env Inject environment variables into the MCP process
--header Set headers for HTTP connections
--scope Define configuration scope: local, user, project
--client-id OAuth client ID (if needed)
--client-secret OAuth client secret
--callback-port Fix the OAuth callback port

For everyday users, the three most common MCP scenarios are:

  • claude mcp list to see which services are connected.
  • claude mcp add to attach a new local or remote MCP.
  • claude mcp remove to clean up unused connections.

5.5 Plugin Commands

Plugins are internal extensions that enhance Claude Code’s own capabilities. You can manage them using either claude plugin or claude plugins.

Basic plugin commands

Command Description
claude plugins list List installed plugins
claude plugins list --json Show the list in JSON format
claude plugins list --available --json Include plugins available from the marketplace
claude plugins install <plugin_name> Install a new plugin
claude plugins enable <plugin_name> Enable an installed plugin
claude plugins disable <plugin_name> Disable a plugin
claude plugins disable -a Disable all enabled plugins
claude plugins update <plugin_name> Update a specific plugin
claude plugins uninstall <plugin_name> Remove a plugin
claude plugins validate <path> Validate a plugin or marketplace manifest

Common scope parameters (for install/enable/disable):

  • user – Apply the change only to the current user.
  • project – Apply the change to the current project.
  • local – More fine‑grained, directory‑level configuration.

5.6 Plugin Marketplace Commands

Marketplaces are sources where plugins are published. These commands let you manage those sources.

Command Description
claude plugins marketplace list List configured marketplaces
claude plugins marketplace list --json Output as JSON
claude plugins marketplace add <source> Add a new marketplace
claude plugins marketplace remove <name> Remove a marketplace
claude plugins marketplace update Update all marketplaces
claude plugins marketplace update <name> Update only a specific marketplace

Parameters for marketplace add:

  • --scope – Write the marketplace definition to user, project, or local.
  • --sparse – If the source is a monorepo, use sparse checkout to fetch only a subset of directories.

6. Slash Commands: Controlling Your Interactive Session

Once you are inside an interactive Claude Code session (by typing claude), you can use slash commands – they all start with a /. These commands let you manage the conversation, adjust settings, and access advanced features.

Note: The exact list of slash commands can vary slightly depending on your version, account permissions, installed plugins, and enabled skills. The commands listed below are those available in a typical installation.

6.1 Context and Session Management

Command What it does When to use
/help Show help and available commands Any time you need a reminder
/exit Leave the current REPL session When you are done
/clear Wipe the conversation history, freeing up context Starting a completely new topic
/compact Compress the context but keep a summary You are near the context limit but want to preserve the gist
/resume Restore a previous conversation Continue an older session
/rewind Roll back the conversation to a specific point You went down a wrong path and want to try again
/fork Create a new session branching from the current point Explore an alternative approach without losing the original
/rename Give the current session a meaningful name Keep your sessions organised
/copy Copy Claude’s last response (or a code block from it) Grab output to paste elsewhere
/export Export the current conversation to a file or clipboard Save a record for later reference
/diff View uncommitted changes and differences between turns Review code modifications step by step

Key distinctions:

  • /clear is a hard reset – Claude forgets everything.
  • /compact is a soft reset – Claude retains a condensed memory.
  • /resume brings back an old conversation.
  • /rewind moves the current conversation backwards in time.
  • /fork creates a parallel branch without affecting the original.

6.2 Environment and Interface Settings

Command Description
/status Show current status: version, model, environment, etc.
/stats View usage statistics and activity
/usage Check plan limits and consumption
/cost Display total cost and time spent in the current session
/config Open the configuration panel
/model Switch to a different model
/plan Enter or view Plan mode
/permissions Manage tool permission rules
/sandbox View or configure sandbox state
/theme Change the UI theme
/vim Toggle between Vim mode and normal editing mode
/fast Toggle Fast Mode
/ide Manage IDE integration and connection status
/add-dir Add a working directory
/statusline Customise the status bar UI
/terminal-setup Install support for Shift+Enter line breaks in the terminal

6.3 Account, Installation, and Connections

Command Description
/login Log in or switch Anthropic accounts
/logout Sign out of the current account
/upgrade Upgrade your plan
/doctor Run installation diagnostics
/init Initialise a new CLAUDE.md file
/desktop Continue the current session on Claude Desktop
/chrome Manage Claude in Chrome settings
/mobile Show a QR code to download the Claude mobile app

6.4 Extension Management

Command Description
/agents Manage agent configurations
/hooks Manage tool event hooks
/skills List currently available skills
/mcp Manage MCP servers (same as terminal subcommand)
/plugin Manage plugins (same as terminal subcommand)
/reload-plugins Apply pending plugin changes to the current session
/install-github-app Connect a GitHub repository to Claude GitHub Actions
/install-slack-app Install the Claude Slack App

6.5 Workflow and Automation

Command Description
/tasks View and manage background tasks
/loop Repeatedly execute a prompt or slash command at a fixed interval
/batch Handle large‑scale changes by first planning, then executing
/review Review a Pull Request
/pr-comments Read GitHub Pull Request comments
/security-review Perform a security check on pending changes
/simplify Analyse code for simplification, reuse, or quality improvements
/debug Enable session‑specific debug logging
/feedback Submit feedback about Claude Code
/stickers Order Claude Code stickers (yes, really)
/insights Generate an analysis report of your Claude Code sessions
/release-notes View the release notes

6.6 Dynamic Skill Commands

These commands are not present on every machine. They appear only when you have installed specific skills, plugins, or extensions. For example, you might see:

  • /x-post-reply-skill – A skill for generating X (Twitter) content.
  • /claude-api – Guidance on using the Claude API or Anthropic SDK.

Remember:

  • Built‑in slash commands are stable and provided by Claude Code itself.
  • Dynamic skill commands are extra capabilities loaded from your environment.

7. Most Useful High‑Frequency Commands

If you want to avoid memorising the whole list, focus on these core commands first.

Terminal High‑Frequency Commands

Command Purpose
claude Start an interactive session
claude -p "task" Run a one‑off task and exit
claude -c Resume the most recent session
claude --help Get overall help
claude mcp list List current MCP connections
claude plugins list --json View plugin list in JSON format

Slash High‑Frequency Commands

Command Purpose
/help Show help and available commands
/clear Clear conversation history
/compact Compress context while preserving summary
/status Check current status
/model Switch models
/permissions Manage tool permission rules
/config Open configuration panel
/mcp Manage MCP servers
/plugin Manage plugins
/review Review a Pull Request

8. Five Pairs That Beginners Often Confuse

Pair 1: claude vs claude -p

  • claude: Interactive session – you talk back and forth.
  • claude -p: One‑shot execution – prints the result and exits immediately.

Pair 2: /clear vs /compact

  • /clear: Completely erases the conversation context – Claude forgets everything.
  • /compact: Shrinks the context but keeps a summary – Claude still remembers the essence.

Pair 3: /resume vs /rewind

  • /resume: Retrieves and restores a past conversation.
  • /rewind: Steps the current conversation backward to an earlier point.

Pair 4: MCP vs Plugins

  • MCP: Connects to external tools and services (like databases, APIs).
  • Plugins: Extend Claude Code’s own functionality (add new slash commands, etc.).

Pair 5: Terminal Subcommands vs Slash Commands

  • Terminal subcommands: Run from your shell, e.g., claude auth login.
  • Slash commands: Run inside an interactive session, e.g., /model.

9. A Suggested Learning Path

If you are learning Claude Code from scratch, follow this sequence. It builds understanding step by step and avoids confusion.

  1. Start with the basics

    • Master claude, claude -p, and claude -c.
    • Learn /help to get help inside a session.
    • Understand the difference between /clear and /compact.

  2. Daily usage

    • Get comfortable with /model to switch models as needed.
    • Use /status to check what is going on.
    • Experiment with /permissions to control tool approvals.

  3. Expand your capabilities

    • Explore auth commands to manage accounts.
    • Add your first MCP with claude mcp add.
    • Install a plugin using claude plugins install.

  4. Embrace engineering workflows

    • Try /review on a real Pull Request.
    • Use /batch for large‑scale file modifications.
    • Run /security-review before committing sensitive changes.

This path ensures you never feel overwhelmed and always have a clear next step.

10. Conclusion: Your Command Map

Claude Code’s command system is not chaotic – it is simply divided into three clean layers:

  • Main command (claude) – the entry point.
  • Subcommands (claude auth, claude mcp, …) – manage features.
  • Slash commands (/help, /clear, …) – control sessions.

You do not need to memorise every command. Build the map in your head first, then learn the commands that match your daily tasks. The rest will come naturally as you need them.

If you want to start using Claude Code right now, these ten commands will get you going:

# Terminal
claude                     # Start interactive session
claude -p "your task"      # One‑shot execution
claude -c                  # Resume last session

# Inside a session (after typing claude)
/help                      # Get help
/clear                     # Clear history
/compact                   # Compact context
/model                     # Switch model
/mcp                       # Manage MCP
/plugin                    # Manage plugins
/review                    # Review a PR

Frequently Asked Questions

Q: Which operating systems does Claude Code support?
A: Claude Code runs on macOS, Linux, and Windows (via WSL). Check the official documentation for the most up‑to‑date list.

Q: How can I see which version of Claude Code I am using?
A: Type claude --version in your terminal, or use /status inside an interactive session.

Q: Where are my Claude Code sessions stored?
A: Sessions are saved locally. The exact location depends on your operating system. Use --no-session-persistence if you do not want to save a session.

Q: What is the difference between MCP and plugins?
A: MCP connects Claude Code to external services (like a database). Plugins add new features to Claude Code itself (like custom slash commands). They serve different purposes.

Q: Should I use /clear or /compact?
A: Use /clear to start a completely fresh topic. Use /compact when you want to free up context space but still want Claude to remember the key points of the conversation.

Q: How do I let Claude Code access files outside my current project?
A: Use the --add-dir parameter when starting Claude, or the /add-dir command inside a session.

Q: What does /permissions do?
A: It lets you set rules for when the AI needs your approval before using tools. You can configure permissions per tool or globally.

Q: Why does my list of slash commands differ from what I see in tutorials?
A: Different plugins, skills, and account permissions can add or remove slash commands. This is normal.

Q: Can Claude Code help me review code?
A: Yes. Use /review for Pull Request reviews and /security-review for security‑focused checks.

Q: How do I handle large, repetitive tasks?
A: The /batch command is designed for exactly that – it plans first, then executes changes systematically.

This guide is based on Claude Code version 2.1.74. Command availability may vary with updates. When in doubt, use /help inside a session to see exactly what is available in your environment.