# CLI Reference

Paperclip CLI now supports both:

- instance setup/diagnostics (`onboard`, `doctor`, `configure`, `env`, `allowed-hostname`, `env-lab`)
- control-plane client operations (issues, approvals, agents, activity, dashboard)

## Base Usage

Use repo script in development:

```sh
pnpm paperclipai --help
```

First-time local bootstrap + run:

```sh
pnpm paperclipai run
```

Choose local instance:

```sh
pnpm paperclipai run --instance dev
```

## Deployment Modes

Mode taxonomy and design intent are documented in `doc/DEPLOYMENT-MODES.md`.

Current CLI behavior:

- `paperclipai onboard` and `paperclipai configure --section server` set deployment mode in config
- server onboarding/configure ask for reachability intent and write `server.bind`
- `paperclipai run --bind <loopback|lan|tailnet>` passes a quickstart bind preset into first-run onboarding when config is missing
- runtime can override mode with `PAPERCLIP_DEPLOYMENT_MODE`
- `paperclipai run` and `paperclipai doctor` still do not expose a direct low-level `--mode` flag

Canonical behavior is documented in `doc/DEPLOYMENT-MODES.md`.

Allow an authenticated/private hostname (for example custom Tailscale DNS):

```sh
pnpm paperclipai allowed-hostname dotta-macbook-pro
```

Bring up the default local SSH fixture for environment testing:

```sh
pnpm paperclipai env-lab up
pnpm paperclipai env-lab doctor
pnpm paperclipai env-lab status --json
pnpm paperclipai env-lab down
```

All client commands support:

- `--data-dir <path>`
- `--api-base <url>`
- `--api-key <token>`
- `--context <path>`
- `--profile <name>`
- `--json`

Company-scoped commands also support `--company-id <id>`.

Use `--data-dir` on any CLI command to isolate all default local state (config/context/db/logs/storage/secrets) away from `~/.paperclip`:

```sh
pnpm paperclipai run --data-dir ./tmp/paperclip-dev
pnpm paperclipai issue list --data-dir ./tmp/paperclip-dev
```

## Context Profiles

Store local defaults in `~/.paperclip/context.json`:

```sh
pnpm paperclipai context set --api-base http://localhost:3100 --company-id <company-id>
pnpm paperclipai context show
pnpm paperclipai context list
pnpm paperclipai context use default
```

To avoid storing secrets in context, set `apiKeyEnvVarName` and keep the key in env:

```sh
pnpm paperclipai context set --api-key-env-var-name PAPERCLIP_API_KEY
export PAPERCLIP_API_KEY=...
```

## Company Commands

```sh
pnpm paperclipai company list
pnpm paperclipai company get <company-id>
pnpm paperclipai company delete <company-id-or-prefix> --yes --confirm <same-id-or-prefix>
```

Examples:

```sh
pnpm paperclipai company delete PAP --yes --confirm PAP
pnpm paperclipai company delete 5cbe79ee-acb3-4597-896e-7662742593cd --yes --confirm 5cbe79ee-acb3-4597-896e-7662742593cd
```

Notes:

- Deletion is server-gated by `PAPERCLIP_ENABLE_COMPANY_DELETION`.
- With agent authentication, company deletion is company-scoped. Use the current company ID/prefix (for example via `--company-id` or `PAPERCLIP_COMPANY_ID`), not another company.

## Issue Commands

```sh
pnpm paperclipai issue list --company-id <company-id> [--status todo,in_progress] [--assignee-agent-id <agent-id>] [--match text]
pnpm paperclipai issue get <issue-id-or-identifier>
pnpm paperclipai issue create --company-id <company-id> --title "..." [--description "..."] [--status todo] [--priority high]
pnpm paperclipai issue update <issue-id> [--status in_progress] [--comment "..."]
pnpm paperclipai issue comment <issue-id> --body "..." [--reopen]
pnpm paperclipai issue checkout <issue-id> --agent-id <agent-id> [--expected-statuses todo,backlog,blocked]
pnpm paperclipai issue release <issue-id>
```

## Agent Commands

```sh
pnpm paperclipai agent list --company-id <company-id>
pnpm paperclipai agent get <agent-id>
pnpm paperclipai agent local-cli <agent-id-or-shortname> --company-id <company-id>
```

`agent local-cli` is the quickest way to run local Claude/Codex manually as a Paperclip agent:

- creates a new long-lived agent API key
- installs missing Paperclip skills into `~/.codex/skills` and `~/.claude/skills`
- prints `export ...` lines for `PAPERCLIP_API_URL`, `PAPERCLIP_COMPANY_ID`, `PAPERCLIP_AGENT_ID`, and `PAPERCLIP_API_KEY`

Example for shortname-based local setup:

```sh
pnpm paperclipai agent local-cli codexcoder --company-id <company-id>
pnpm paperclipai agent local-cli claudecoder --company-id <company-id>
```

## Skills Commands

`paperclipai skills` covers three distinct operations:

1. **Company install** — adds or updates a row in `company_skills` for the
   whole company. This is what `skills install`, `skills import`, `skills create`,
   and `skills scan-projects` do.
2. **Agent attach** — replaces an agent's *desired* company skill set
   (`skills agent sync`/`clear`). This is a desired-state operation on the
   agent's adapter config; it does not change the company library.
3. **Adapter runtime sync** — the adapter reconciles the desired skill set
   with files on disk and reports an `AgentSkillSnapshot` (`skills agent list`).
   `skills agent sync` triggers this automatically after updating desired state.

Required Paperclip runtime skills (heartbeat, etc.) remain server-enforced and
are added on top of whatever the desired set names.

### Catalog (app-shipped skills)

The Paperclip app ships a curated catalog under `@paperclipai/skills-catalog`.
Browse and inspect commands never mutate company state; `install` adds a catalog
skill to the company library.

```sh
pnpm paperclipai skills browse [--kind bundled|optional] [--category <slug>] [--query <text>]
pnpm paperclipai skills search "<text>" [--kind bundled|optional] [--category <slug>]
pnpm paperclipai skills inspect <catalog-id-or-key-or-slug>
pnpm paperclipai skills install <catalog-id-or-key-or-slug> [--as <slug>] [--force] --company-id <company-id>
```

Catalog semantics:

- **Bundled** skills live in `packages/skills-catalog/catalog/bundled/<category>/<slug>`
  and are recommended defaults for most companies. They use canonical key
  `paperclipai/bundled/<category>/<slug>`.
- **Optional** skills live in `packages/skills-catalog/catalog/optional/<category>/<slug>`
  and are role-specific or domain-specific (browser, AWS ops, etc.). Same key
  shape with `optional` in place of `bundled`.
- `skills install` materializes the catalog files into a company-managed skill
  directory and records provenance (`catalogId`, `catalogKey`, `packageVersion`,
  `originHash`, …) so future updates and audit decisions stay consistent.
- `--as <slug>` overrides the company skill slug. `--force` may replace a
  same-key catalog-managed skill but never bypasses hard validation or hard-stop
  audit findings.

Examples:

```sh
pnpm paperclipai skills browse --kind bundled --company-id <company-id>
pnpm paperclipai skills search "pull request" --kind bundled
pnpm paperclipai skills inspect github-pr-workflow
pnpm paperclipai skills install github-pr-workflow --company-id <company-id>
pnpm paperclipai skills install paperclipai:optional:browser:agent-browser --company-id <company-id>
```

External GitHub, skills.sh, local-path, and URL sources still go through
`skills import`; catalog commands are for the app-shipped catalog only.

### Company library

```sh
pnpm paperclipai skills list --company-id <company-id>
pnpm paperclipai skills show <skill-id-or-key-or-slug> --company-id <company-id>
pnpm paperclipai skills file <skill-id-or-key-or-slug> [--path SKILL.md] --company-id <company-id>
pnpm paperclipai skills import <source> --company-id <company-id>
pnpm paperclipai skills create --name "Review PRs" [--slug review-prs] [--description "..."] [--body-file SKILL.md] --company-id <company-id>
pnpm paperclipai skills scan-projects [--project-id <id>...] [--workspace-id <id>...] --company-id <company-id>
pnpm paperclipai skills check [skill-id-or-key-or-slug] --company-id <company-id>
pnpm paperclipai skills update <skill-id-or-key-or-slug> [--force] --company-id <company-id>
pnpm paperclipai skills update --all [--force] --company-id <company-id>
pnpm paperclipai skills audit [skill-id-or-key-or-slug] --company-id <company-id>
pnpm paperclipai skills reset <skill-id-or-key-or-slug> [--yes] [--force] --company-id <company-id>
pnpm paperclipai skills remove <skill-id-or-key-or-slug> --yes --company-id <company-id>
```

`skills import <source>` accepts a skills.sh URL, the equivalent
`<owner>/<repo>/<skill>` shorthand, a GitHub URL, a local path, or an
`npx skills add …` command. See `references/company-skills.md` in the agent
skill bundle for the source-type table.

`skills check`, `skills update`, `skills audit`, and `skills reset` are the
maintenance loop for catalog-installed skills:

- `check` reports whether each skill's installed bytes match its pinned origin
  (`hasUpdate`, `installedHash`, `originHash`, `updateHoldReason`,
  `auditVerdict`).
- `update` installs the pinned update through the existing install-update API.
  `--all` checks every company skill and updates only those with
  `hasUpdate=true`. `--force` discards local-modification or soft-audit holds;
  hard-stop audit findings still block the update.
- `audit` re-scans installed bytes and reports findings without executing
  anything.
- `reset` reinstalls a catalog-managed skill from its pinned origin, discarding
  local edits. Prompts in a TTY; requires `--yes` for non-interactive use.

### Agent attach

```sh
pnpm paperclipai skills agent list <agent-id-or-shortname> --company-id <company-id>
pnpm paperclipai skills agent sync <agent-id-or-shortname> --skill <skill-id-or-key-or-slug> [--skill <skill-id-or-key-or-slug>...] --company-id <company-id>
pnpm paperclipai skills agent clear <agent-id-or-shortname> --yes --company-id <company-id>
```

`skills agent sync` replaces the agent's non-required desired skill set (it is
not additive) and returns the resulting adapter `AgentSkillSnapshot`.
`skills agent clear` sends an empty desired list. Required Paperclip skills are
still enforced by the server in both cases.

### Notes

- Skill references accept company skill `id`, canonical `key`, or unique
  `slug`; catalog references accept catalog `id`, `key`, or unique `slug`.
- `skills file` prints raw file content in human mode so it can be piped.
- `skills create --body-file -` reads the skill markdown body from stdin.
- `skills remove`, `skills reset`, and `skills agent clear` prompt in a TTY and
  require `--yes` in non-interactive use.
- `--json` prints the raw API result for each command.

## Secrets Commands

```sh
pnpm paperclipai secrets list --company-id <company-id>
pnpm paperclipai secrets declarations --company-id <company-id> [--include agents,projects] [--kind secret]
pnpm paperclipai secrets create --company-id <company-id> --name anthropic-api-key --value-env ANTHROPIC_API_KEY
pnpm paperclipai secrets link --company-id <company-id> --name prod-stripe-key --provider aws_secrets_manager --external-ref <provider-ref>
pnpm paperclipai secrets doctor --company-id <company-id>
pnpm paperclipai secrets migrate-inline-env --company-id <company-id> [--apply]
```

Secret listing and declarations never print secret values. `create` accepts
`--value-env` so shell history does not capture the value. `link` records
provider-owned references without copying the secret value into Paperclip.
For AWS-backed secrets, `secrets doctor` reports missing non-secret provider
env and the expected AWS SDK runtime credential source; do not store AWS
bootstrap credentials in Paperclip secrets.

Per-company provider vaults (multiple vault instances per provider, default
vault selection, coming-soon GCP/Vault) are configured from the board UI under
`Company Settings → Secrets → Provider vaults` or through
`/api/companies/{companyId}/secret-provider-configs`. There is no CLI surface
for vault management today. See the
[secrets deploy guide](../docs/deploy/secrets.md#provider-vaults) and
[API reference](../docs/api/secrets.md#provider-vaults) for the contract.

## Approval Commands

```sh
pnpm paperclipai approval list --company-id <company-id> [--status pending]
pnpm paperclipai approval get <approval-id>
pnpm paperclipai approval create --company-id <company-id> --type hire_agent --payload '{"name":"..."}' [--issue-ids <id1,id2>]
pnpm paperclipai approval approve <approval-id> [--decision-note "..."]
pnpm paperclipai approval reject <approval-id> [--decision-note "..."]
pnpm paperclipai approval request-revision <approval-id> [--decision-note "..."]
pnpm paperclipai approval resubmit <approval-id> [--payload '{"...":"..."}']
pnpm paperclipai approval comment <approval-id> --body "..."
```

## Activity Commands

```sh
pnpm paperclipai activity list --company-id <company-id> [--agent-id <agent-id>] [--entity-type issue] [--entity-id <id>]
```

## Dashboard Commands

```sh
pnpm paperclipai dashboard get --company-id <company-id>
```

## Heartbeat Command

`heartbeat run` now also supports context/api-key options and uses the shared client stack:

```sh
pnpm paperclipai heartbeat run --agent-id <agent-id> [--api-base http://localhost:3100] [--api-key <token>]
```

## Local Storage Defaults

Local Paperclip data lives under the selected instance root. `PAPERCLIP_HOME` chooses the home directory and `PAPERCLIP_INSTANCE_ID` chooses the instance.

```text
~/.paperclip/                                     # PAPERCLIP_HOME
└── instances/
    └── default/                                  # instance root (PAPERCLIP_INSTANCE_ID)
        ├── config.json                           # runtime config
        ├── .env                                  # instance env file
        ├── db/                                   # embedded PostgreSQL data
        ├── data/
        │   ├── storage/                          # local_disk uploads
        │   └── backups/                          # automatic DB backups
        ├── logs/
        ├── secrets/
        │   └── master.key                        # local_encrypted master key
        ├── workspaces/                           # default agent workspaces
        ├── projects/                             # project execution workspaces
        ├── companies/                            # per-company adapter homes (e.g. codex-home)
        └── codex-home/                           # per-instance codex home (when not company-scoped)
```

Default paths for the canonical install:

- config: `~/.paperclip/instances/default/config.json`
- embedded db: `~/.paperclip/instances/default/db`
- logs: `~/.paperclip/instances/default/logs`
- storage: `~/.paperclip/instances/default/data/storage`
- secrets key: `~/.paperclip/instances/default/secrets/master.key`

Override base home or instance with env vars:

```sh
PAPERCLIP_HOME=/custom/home PAPERCLIP_INSTANCE_ID=dev pnpm paperclipai run
```

## Storage Configuration

Configure storage provider and settings:

```sh
pnpm paperclipai configure --section storage
```

Supported providers:

- `local_disk` (default; local single-user installs)
- `s3` (S3-compatible object storage)