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paperclip/doc/CLI.md
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Dotta 778e775c35 Add secrets provider vaults and remote import (#5429) 
## Thinking Path

> - Paperclip orchestrates AI-agent companies and needs secrets handling
to work across local development, hosted operators, and governed agent
execution.
> - The affected subsystem is the company-scoped secrets control plane:
database schema, server services/routes, CLI workflows, and the Secrets
settings UI.
> - The gap was that secrets were local-only and operators could not
manage provider vaults or import existing remote references without
exposing plaintext.
> - This branch adds provider vault configuration plus an AWS Secrets
Manager remote-import path while preserving company boundaries, binding
context, and audit trails.
> - I kept the PR to a single branch PR, removed unrelated
lockfile/package drift, rebased the full branch onto the current
`public-gh/master`, and addressed fresh Greptile findings.
> - The benefit is a reviewable implementation of provider-backed
secrets with focused tests covering provider selection, import
conflicts, deleted secret reuse, rotation guards, and AWS signing
behavior.

## What Changed

- Added provider vault support for company secrets, including provider
config storage, default vault handling, health checks, binding usage,
access events, and remote import preview/commit.
- Added an AWS Secrets Manager provider using SigV4 request signing,
bounded request timeouts, namespace guardrails, cached runtime
credential resolution, and external-reference linking without plaintext
reads.
- Added Secrets UI surfaces for vault management and remote import, plus
CLI/API documentation for setup and operations.
- Stabilized routine webhook secret binding paths and SSH
environment-driver fixture bindings discovered during verification.
- Addressed Greptile and CI findings: no lockfile/package drift,
monotonic migration metadata, disabled-vault default races, soft-deleted
secret hiding/recreate behavior, remove behavior with disabled vaults,
soft-deleted external-reference re-import, non-active rotation guards,
managed-secret soft deletion through PATCH, and per-call AWS SDK
credential client churn.
- Rebased this branch onto `public-gh/master` at `0e1a5828` and
force-pushed with lease to keep this as the single PR for the branch.

## Verification

- `git fetch public-gh master`
- `git rebase public-gh/master`
- `git diff --name-only public-gh/master...HEAD | grep
'^pnpm-lock\.yaml$' || true` confirmed `pnpm-lock.yaml` is not in the PR
diff.
- Confirmed migration ordering: master ends at `0081_optimal_dormammu`;
this PR adds `0082_dry_vision` and
`0083_company_secret_provider_configs`.
- Inspected migrations for repeat safety: new tables/indexes use `IF NOT
EXISTS`; foreign keys are guarded by `DO $$ ... IF NOT EXISTS`; column
additions use `ADD COLUMN IF NOT EXISTS`.
- `pnpm -r typecheck` passed before the Greptile follow-up commits.
- `pnpm test:run` ran the full stable Vitest path before the Greptile
follow-up commits; it completed with 3 timing-related failures under
parallel load: `codex-local-execute.test.ts`,
`cursor-local-execute.test.ts`, and `environment-service.test.ts`.
- `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/codex-local-execute.test.ts
src/__tests__/cursor-local-execute.test.ts
src/__tests__/environment-service.test.ts` passed on targeted rerun
(`24/24`).
- `pnpm build` passed before the Greptile follow-up commits. Vite
reported existing chunk-size/dynamic-import warnings.
- After Greptile follow-up commits: `pnpm --filter @paperclipai/server
exec vitest run src/__tests__/secrets-service.test.ts` passed (`26/26`).
- After Greptile follow-up commits: `pnpm --filter @paperclipai/server
exec vitest run src/__tests__/aws-secrets-manager-provider.test.ts
src/__tests__/secrets-service.test.ts` passed (`39/39`).
- After Greptile follow-up commits: `pnpm --filter @paperclipai/server
typecheck` passed.
- Captured Storybook screenshots from `ui/storybook-static` for visual
review.
- Latest PR checks on `5ca3a5cf`: `policy`, serialized server suites
1/4-4/4, `Canary Dry Run`, `e2e`, `security/snyk`, and `Greptile Review`
pass; aggregate `verify` is still registering the completed child
checks.
- Greptile review loop continued through the latest requested pass; all
Greptile review threads are resolved and the latest `Greptile Review`
check on `5ca3a5cf` passed with 0 comments added.

## Screenshots

Before: the provider-vault and remote-import surfaces did not exist on
`master`; these are after-state screenshots from the Storybook fixtures.

![Secrets
inventory](https://raw.githubusercontent.com/paperclipai/paperclip/PAP-2339-secrets-make-a-plan/doc/pr/5429/secrets-inventory.png)

![Secret binding
picker](https://raw.githubusercontent.com/paperclipai/paperclip/PAP-2339-secrets-make-a-plan/doc/pr/5429/secret-binding-picker.png)

![Environment editor with
secrets](https://raw.githubusercontent.com/paperclipai/paperclip/PAP-2339-secrets-make-a-plan/doc/pr/5429/env-editor-with-secrets.png)

## Risks

- Migration risk: this adds new secret provider tables and extends
existing secret rows. The migrations were checked for monotonic ordering
and idempotent guards, but reviewers should still inspect upgrade
behavior carefully.
- Provider risk: AWS support uses direct SigV4 requests. Automated tests
cover signing, request timeouts, vault-config selection, namespace
guardrails, pending-version archival, sanitized provider errors, and
service-level cleanup paths. A real-vault AWS smoke test remains
deployment validation for an operator with AWS credentials rather than
an unverified merge blocker in this local branch.
- UI risk: the Secrets page and import dialog are large new surfaces;
screenshots are included above for reviewer inspection.
- Verification risk: the full local stable test command hit
parallel-load timing failures, although the exact failed files passed
when rerun directly.
- Operational risk: remote import intentionally avoids plaintext reads;
operators must understand that imported external references resolve at
runtime and may fail if AWS permissions change.

> For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and
discuss it in `#dev` before opening the PR. Feature PRs that overlap
with planned core work may need to be redirected — check the roadmap
first. See `CONTRIBUTING.md`.

## Model Used

- OpenAI Codex, GPT-5 coding agent with local shell/tool use in the
Paperclip worktree. Exact context-window size was not exposed by the
runtime.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [ ] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
2026-05-09 18:22:17 -05:00

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# 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>
```
## 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
Default local instance root is `~/.paperclip/instances/default`:
- 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)
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