MCPInstall

cli-reference

Claude Code CLI commands, flags, headless mode, and automation patterns

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Install

Works with every agent the skills CLI supports.

npx skills add https://github.com/parcadei/continuous-claude-v3 --skill cli-reference
  1. 01

    Install

    Run the command in your project. The CLI asks which agents to install for.

  2. 02

    Describe the task

    Ask your agent for something this skill covers. It loads cli-reference automatically when relevant.

  3. 03

    Review the result

    The agent follows the SKILL.md steps, scripts and references bundled with the skill.

SKILL.md

The instructions your agent reads when the skill is triggered.

CLI Reference

Complete reference for Claude Code command-line interface.

When to Use

  • "What CLI flags are available?"
  • "How do I use headless mode?"
  • "Claude in automation/CI/CD"
  • "Output format options"
  • "System prompt via CLI"
  • "How do I spawn agents properly?"

Core Commands

CommandDescriptionExample
claudeStart interactive REPLclaude
claude "query"REPL with initial promptclaude "explain this project"
claude -p "query"Headless mode (SDK)claude -p "explain function"
cat file | claude -pProcess piped contentcat logs.txt | claude -p "explain"
claude -cContinue most recentclaude -c
claude -c -p "query"Continue via SDKclaude -c -p "check types"
claude -r "id" "query"Resume sessionclaude -r "auth" "finish PR"
claude updateUpdate versionclaude update
claude mcpConfigure MCP serversSee MCP docs

Session Control

FlagDescriptionExample
--continue, -cLoad most recent conversationclaude --continue
--resume, -rResume session by ID/nameclaude --resume auth-refactor
--session-idUse specific UUIDclaude --session-id "550e8400-..."
--fork-sessionCreate new session on resumeclaude --resume abc --fork-session

Headless Mode (Critical for Agents)

FlagDescriptionExample
--print, -pNon-interactive, exit afterclaude -p "query"
--output-formattext, json, stream-jsonclaude -p --output-format json
--max-turnsLimit agentic turnsclaude -p --max-turns 100 "query"
--verboseFull turn-by-turn outputclaude --verbose
--dangerously-skip-permissionsSkip permission promptsclaude -p --dangerously-skip-permissions
--include-partial-messagesInclude streaming eventsclaude -p --output-format stream-json --include-partial-messages
--input-formatInput format (text/stream-json)claude -p --input-format stream-json

Tool Control

FlagDescriptionExample
--allowedToolsAuto-approve these tools"Bash(git log:*)" "Read"
--disallowedToolsBlock these tools"Bash(rm:*)" "Edit"
--toolsOnly allow these tools--tools "Bash,Edit,Read"

Subagent Definition (--agents flag)

Define custom subagents inline via JSON:

claude --agents '{
  "code-reviewer": {
    "description": "Expert code reviewer. Use proactively after code changes.",
    "prompt": "You are a senior code reviewer. Focus on code quality and security.",
    "tools": ["Read", "Grep", "Glob", "Bash"],
    "model": "sonnet"
  },
  "debugger": {
    "description": "Debugging specialist for errors and test failures.",
    "prompt": "You are an expert debugger. Analyze errors and provide fixes."
  }
}'

Agent Fields

FieldRequiredDescription
descriptionYesWhen to invoke this agent
promptYesSystem prompt for behavior
toolsNoAllowed tools (inherits all if omitted)
modelNosonnet, haiku, or claude-opus-4-5-20251101

Key Insight

When Lead uses Task tool, it auto-spawns from these definitions. No manual spawn needed.

System Prompt Customization

FlagBehaviorModes
--system-promptReplace entire promptInteractive + Print
--system-prompt-fileReplace from filePrint only
--append-system-promptAppend to default (recommended)Interactive + Print

Use --append-system-prompt for most cases - preserves Claude Code capabilities.

Model Selection

FlagDescriptionExample
--modelSet model for session--model claude-sonnet-4-5
--fallback-modelFallback if default overloaded--fallback-model sonnet

Aliases: sonnet, opus, haiku

MCP Configuration

FlagDescriptionExample
--mcp-configLoad MCP servers from JSON--mcp-config ./mcp.json
--strict-mcp-configOnly use these MCP servers--strict-mcp-config --mcp-config ./mcp.json

Advanced Flags

FlagDescriptionExample
--add-dirAdd working directories--add-dir ../apps ../lib
--agentSpecify agent for session--agent my-custom-agent
--permission-modeStart in permission mode--permission-mode plan
--permission-prompt-toolMCP tool for permissions--permission-prompt-tool mcp_auth
--plugin-dirLoad plugins from directory--plugin-dir ./my-plugins
--settingsLoad settings from file/JSON--settings ./settings.json
--setting-sourcesWhich settings to load--setting-sources user,project
--betasBeta API headers--betas interleaved-thinking
--debugEnable debug mode--debug "api,hooks"
--ideAuto-connect to IDE--ide
--chromeEnable Chrome integration--chrome
--no-chromeDisable Chrome for session--no-chrome
--enable-lsp-loggingVerbose LSP debugging--enable-lsp-logging
--version, -vOutput versionclaude -v

Output Formats

JSON (for parsing)

claude -p "query" --output-format json
# {"result": "...", "session_id": "...", "usage": {...}}

Streaming (for real-time monitoring)

claude -p "query" --output-format stream-json
# Newline-delimited JSON events

Structured Output (schema validation)

claude -p "Extract data" \
  --output-format json \
  --json-schema '{"type":"object","properties":{...}}'

Headless Agent Pattern (CRITICAL)

Proper headless agent spawn:

claude -p "$TASK_PROMPT" \
  --session-id "$UUID" \
  --dangerously-skip-permissions \
  --max-turns 100 \
  --output-format stream-json \
  --agents '{...}' \
  --append-system-prompt "Context: ..."

Missing any of these causes hangs:

  • --session-id - Track the session
  • --dangerously-skip-permissions - Headless requires this
  • --max-turns - Prevents infinite loops

Common Patterns

CI/CD Automation

claude -p "Run tests and fix failures" \
  --dangerously-skip-permissions \
  --max-turns 50 \
  --output-format json | jq '.result'

Piped Input

cat error.log | claude -p "Find root cause"
gh pr diff | claude -p "Review for security"

Multi-turn Session

id=$(claude -p "Start task" --output-format json | jq -r '.session_id')
claude -p "Continue" --resume "$id"

Stream Monitoring

claude -p "Long task" \
  --output-format stream-json \
  --include-partial-messages | while read -r line; do
    echo "$line" | jq '.type'
done

Keyboard Shortcuts (Interactive)

ShortcutAction
Ctrl+CCancel current
Ctrl+DExit
Ctrl+RReverse search history
Esc EscRewind changes
Shift+TabToggle permission mode

Quick Commands

PrefixAction
/Slash command
!Bash mode
#Add to memory
@File mention

FAQ

What does the cli-reference skill do?

Claude Code CLI commands, flags, headless mode, and automation patterns

How do I install cli-reference?

Run npx skills add https://github.com/parcadei/continuous-claude-v3 --skill cli-reference in your project. The skills CLI detects the agents you use and copies the skill into the right folder. For Claude Code you can also place the skill folder at ~/.claude/skills/cli-reference/ (personal) or .claude/skills/cli-reference/ (project).

Which AI agents can use cli-reference?

Any agent that supports the open Agent Skills format (a folder with a SKILL.md file), including Claude Code, Codex, Cursor, GitHub Copilot, Gemini CLI, Windsurf, Cline, OpenCode and more.

Is cli-reference safe to install?

No partner security audit is available yet. Skills can run commands and scripts, so read the SKILL.md and any bundled files before installing.

Who maintains cli-reference?

It is published by parcadei in parcadei/continuous-claude-v3. It has 489 recorded installs.

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