cli-reference

What the source does

• FilesystemNone observedNo reads or writes in the source
• NetworkNone observedNo outbound calls in the source
• ShellNone observedNo commands run in the source
• DependenciesPinnedNothing floats
• SecretsNone foundNo keys in source

Five audit layers

Gates applied: no behavioural pass.

.claude/scripts/mcp

"prompt": "You are a senior code reviewer. Focus on code quality and security.",

Audit 0.4.1 · source sha 79ffdab59d4c · 31 Oct 2026Report an issue or request a re-scan

• Publisherparcadei GitHub userOwner of the repository this skill is read from
• Source folderparcadei/continuous-claude-v3/.claude/skills/cli-referenceThe exact folder we audited
• LicenceMITAs the repository states it
• Commit pinned for this verdict79ffdab59d4cA new audit runs when the source changes
• Repository statusNot archivedLast push 277 days ago
• Sandboxed runNot runSkills are read, not executed; layer L4 is skipped

Its description: Claude Code CLI commands, flags, headless mode, and automation patterns

---
name: cli-reference
description: Claude Code CLI commands, flags, headless mode, and automation patterns
allowed-tools: [Read]
---

# 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

| Command | Description | Example |
|---------|-------------|---------|
| `claude` | Start interactive REPL | `claude` |
| `claude "query"` | REPL with initial prompt | `claude "explain this project"` |
| `claude -p "query"` | Headless mode (SDK) | `claude -p "explain function"` |
| `cat file \| claude -p` | Process piped content | `cat logs.txt \| claude -p "explain"` |
| `claude -c` | Continue most recent | `claude -c` |
| `claude -c -p "query"` | Continue via SDK | `claude -c -p "check types"` |
| `claude -r "id" "query"` | Resume session | `claude -r "auth" "finish PR"` |
| `claude update` | Update version | `claude update` |
| `claude mcp` | Configure MCP servers | See MCP docs |

## Session Control

| Flag | Description | Example |
|------|-------------|---------|
| `--continue, -c` | Load most recent conversation | `claude --continue` |
| `--resume, -r` | Resume session by ID/name | `claude --resume auth-refactor` |
| `--session-id` | Use specific UUID | `claude --session-id "550e8400-..."` |
| `--fork-session` | Create new session on resume | `claude --resume abc --fork-session` |

## Headless Mode (Critical for Agents)

| Flag | Description | Example |
|------|-------------|---------|
| `--print, -p` | Non-interactive, exit after | `claude -p "query"` |
| `--output-format` | `text`, `json`, `stream-json` | `claude -p --output-format json` |
| `--max-turns` | Limit agentic turns | `claude -p --max-turns 100 "query"` |
| `--verbose` | Full turn-by-turn output | `claude --verbose` |
| `--dangerously-skip-permissions` | Skip permission prompts | `claude -p --dangerously-skip-permissions` |
| `--include-partial-messages` | Include streaming events | `claude -p --output-format stream-json --include-partial-messages` |
| `--input-format` | Input format (text/stream-json) | `claude -p --input-format stream-json` |

## Tool Control

| Flag | Description | Example |
|------|-------------|---------|
| `--allowedTools` | Auto-approve these tools | `"Bash(git log:*)" "Read"` |
| `--disallowedTools` | Block these tools | `"Bash(rm:*)" "Edit"` |
| `--tools` | Only allow these tools | `--tools "Bash,Edit,Read"` |

## Subagent Definition (--agents flag)

Define custom subagents inline via JSON:

```bash
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

| Field | Required | Description |
|-------|----------|-------------|
| `description` | Yes | When to invoke this agent |
| `prompt` | Yes | System prompt for behavior |
| `tools` | No | Allowed tools (inherits all if omitted) |
| `model` | No | `sonnet`, `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

| Flag | Behavior | Modes |
|------|----------|-------|
| `--system-prompt` | **Replace** entire prompt | Interactive + Print |
| `--system-prompt-file` | **Replace** from file | Print only |
| `--append-system-prompt` | **Append** to default (recommended) | Interactive + Print |

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

## Model Selection

| Flag | Description | Example |
|------|-------------|---------|
| `--model` | Set model for session | `--model claude-sonnet-4-5` |
| `--fallback-model` | Fallback if default overloaded | `--fallback-model sonnet` |

Aliases: `sonnet`, `opus`, `haiku`

## MCP Configuration

| Flag | Description | Example |
|------|-------------|---------|
| `--mcp-config` | Load MCP servers from JSON | `--mcp-config ./mcp.json` |
| `--strict-mcp-config` | Only use these MCP servers | `--strict-mcp-config --mcp-config ./mcp.json` |

## Advanced Flags

| Flag | Description | Example |
|------|-------------|---------|
| `--add-dir` | Add working directories | `--add-dir ../apps ../lib` |
| `--agent` | Specify agent for session | `--agent my-custom-agent` |
| `--permission-mode` | Start in permission mode | `--permission-mode plan` |
| `--permission-prompt-tool` | MCP tool for permissions | `--permission-prompt-tool mcp_auth` |
| `--plugin-dir` | Load plugins from directory | `--plugin-dir ./my-plugins` |
| `--settings` | Load settings from file/JSON | `--settings ./settings.json` |
| `--setting-sources` | Which settings to load | `--setting-sources user,project` |
| `--betas` | Beta API headers | `--betas interleaved-thinking` |
| `--debug` | Enable debug mode | `--debug "api,hooks"` |
| `--ide` | Auto-connect to IDE | `--ide` |
| `--chrome` | Enable Chrome integration | `--chrome` |
| `--no-chrome` | Disable Chrome for session | `--no-chrome` |
| `--enable-lsp-logging` | Verbose LSP debugging | `--enable-lsp-logging` |
| `--version, -v` | Output version | `claude -v` |

## Output Formats

### JSON (for parsing)
```bash
claude -p "query" --output-format json
# {"result": "...", "session_id": "...", "usage": {...}}
```

### Streaming (for real-time monitoring)
```bash
claude -p "query" --output-format stream-json
# Newline-delimited JSON events
```

### Structured Output (schema validation)
```bash
claude -p "Extract data" \
  --output-format json \
  --json-schema '{"type":"object","properties":{...}}'
```

## Hea

Excerpt, first 6,000 characters of SKILL.md, verbatim from the audited commit. It is text from someone else’s repository, quoted so you can judge it before your agent reads it.

1. 2026-10-31
   ✓SAFE B 89 / 100

   first audit · source 79ffdab59d4c

Questions about cli-reference

• github.com/parcadei/continuous-claude-v3/tree/main/.claude/skill — the audited source at commit 79ffdab59d4c and every finding aboveObserved · 31 Oct 2026

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