paperclip/docs/cli/overview.md

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---
title: CLI Overview
summary: CLI installation and setup
---
The Paperclip CLI handles instance setup, diagnostics, and control-plane operations.
## Usage
```sh
pnpm paperclipai --help
```
## Global Options
All commands support:
| Flag | Description |
|------|-------------|
| `--data-dir <path>` | Local Paperclip data root (isolates from `~/.paperclip`) |
| `--api-base <url>` | API base URL |
| `--api-key <token>` | API authentication token |
| `--context <path>` | Context file path |
| `--profile <name>` | Context profile name |
| `--json` | Output as JSON |
Company-scoped commands also accept `--company-id <id>`.
For clean local instances, pass `--data-dir` on the command you run:
```sh
npx paperclipai run --data-dir ./tmp/paperclip-dev
```
## Context Profiles
Store defaults to avoid repeating flags:
```sh
# Set defaults
npx paperclipai context set --api-base http://localhost:3100 --company-id <id>
# View current context
pnpm paperclipai context show
# List profiles
pnpm paperclipai context list
# Switch profile
npx paperclipai context use default
```
To avoid storing secrets in context, use an env var:
```sh
npx paperclipai context set --api-key-env-var-name PAPERCLIP_API_KEY
export PAPERCLIP_API_KEY=...
```
Secret operations are available under `paperclipai secrets`:
```sh
npx paperclipai secrets declarations --company-id <company-id> --kind secret
npx paperclipai secrets create --company-id <company-id> --name anthropic-api-key --value-env ANTHROPIC_API_KEY
npx paperclipai secrets link --company-id <company-id> --name prod-stripe-key --provider aws_secrets_manager --external-ref <provider-ref>
npx paperclipai secrets doctor --company-id <company-id>
npx paperclipai secrets migrate-inline-env --company-id <company-id> --apply
```
Context is stored at `~/.paperclip/context.json`.
## Command Categories
The CLI has two categories:
1. **[Setup commands](/cli/setup-commands)** — instance bootstrap, diagnostics, configuration
2. **[Control-plane commands](/cli/control-plane-commands)** — issues, agents, approvals, activity