> ## Documentation Index
> Fetch the complete documentation index at: https://docs.thinkingmach.com/llms.txt
> Use this file to discover all available pages before exploring further.

# Setup Commands

Instance setup and diagnostics commands.

## `paperclipai run`

One-command bootstrap and start:

```sh theme={null}
pnpm paperclipai run
```

Does:

1. Auto-onboards if config is missing
2. Runs `paperclipai doctor` with repair enabled
3. Starts the server when checks pass

Choose a specific instance:

```sh theme={null}
npx paperclipai run --instance dev
```

## `paperclipai onboard`

Interactive first-time setup:

```sh theme={null}
pnpm paperclipai onboard
```

If Paperclip is already configured, rerunning `onboard` keeps the existing config in place. Use `paperclipai configure` to change settings on an existing install.

First prompt:

1. `Quickstart` (recommended): local defaults (embedded database, no LLM provider, local disk storage, default secrets)
2. `Advanced setup`: full interactive configuration

Start immediately after onboarding:

```sh theme={null}
pnpm paperclipai onboard --run
```

Non-interactive defaults + immediate start (opens browser on server listen):

```sh theme={null}
pnpm paperclipai onboard --yes
```

On an existing install, `--yes` now preserves the current config and just starts Paperclip with that setup.

## `paperclipai doctor`

Health checks with optional auto-repair:

```sh theme={null}
pnpm paperclipai doctor
pnpm paperclipai doctor --repair
```

Validates:

* Server configuration
* Database connectivity
* Secrets adapter configuration, including AWS Secrets Manager non-secret env
  config when selected
* Storage configuration
* Missing key files

## `paperclipai configure`

Update configuration sections:

```sh theme={null}
pnpm paperclipai configure --section server
pnpm paperclipai configure --section secrets
pnpm paperclipai configure --section storage
```

`--section secrets` updates the deployment-level provider used as the fallback
for secrets that do not target a specific company vault. Per-company provider
vaults (named instances, default vault selection, multiple vaults per provider,
coming-soon GCP/Vault) live in the board UI under
`Company Settings → Secrets → Provider vaults` and the
`/api/companies/{companyId}/secret-provider-configs` API.

## `paperclipai env`

Show resolved environment configuration:

```sh theme={null}
pnpm paperclipai env
```

This now includes bind-oriented deployment settings such as `PAPERCLIP_BIND` and `PAPERCLIP_BIND_HOST` when configured.

## `paperclipai allowed-hostname`

Allow a private hostname for authenticated/private mode:

```sh theme={null}
npx paperclipai allowed-hostname my-tailscale-host
```

## Local Storage Paths

| Data        | Default Path                                        |
| ----------- | --------------------------------------------------- |
| Config      | `~/.paperclip/instances/default/config.json`        |
| Database    | `~/.paperclip/instances/default/db`                 |
| Logs        | `~/.paperclip/instances/default/logs`               |
| Storage     | `~/.paperclip/instances/default/data/storage`       |
| Secrets key | `~/.paperclip/instances/default/secrets/master.key` |

Override with:

```sh theme={null}
PAPERCLIP_HOME=/custom/home PAPERCLIP_INSTANCE_ID=dev pnpm paperclipai run
```

Or pass `--data-dir` directly on any command:

```sh theme={null}
npx paperclipai run --data-dir ./tmp/paperclip-dev
npx paperclipai doctor --data-dir ./tmp/paperclip-dev
```