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Dotta 0096b56a1c [codex] Add LLM Wiki plugin host support (#5597) 
## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies.
> - The plugin system needs host contracts and runtime support before
large plugins can integrate cleanly.
> - The source branch mixed the LLM Wiki package with supporting
host/runtime work, managed plugin skills, root-level storage spaces, and
a bookmarks reference plugin.
> - [PAP-9173](/PAP/issues/PAP-9173) asked for the current branch to be
split by file boundary: plugin package separately from everything else.
> - [PAP-9188](/PAP/issues/PAP-9188) clarified that LLM Wiki may have
plugin-local spaces, but Paperclip core should not reorganize top-level
local storage into spaces.
> - Follow-up review clarified that the bookmarks example should not
ship in this PR either.
> - This pull request contains the
non-`packages/plugins/plugin-llm-wiki/` host/runtime work, keeps runtime
state under the selected Paperclip instance root, and no longer includes
the bookmarks example.

## What Changed

- Added/updated plugin host contracts, SDK types, worker RPC plumbing,
managed plugin skill support, and related server tests.
- Removed the bookmarks example plugin package and its
bundled-example/workspace references.
- Removed the root-level local spaces CLI/migration surface and restored
instance-root runtime defaults for config, db, logs, storage, secrets,
workspaces, projects, and adapter homes.
- Replaced shared root `space-paths` helpers with `home-paths` helpers
for core runtime storage.
- Tightened stranded recovery unique-conflict detection so concurrent
recovery scans reuse the raced recovery issue when Postgres errors are
wrapped.
- Kept `packages/plugins/plugin-llm-wiki/` out of this PR diff;
plugin-local spaces remain in the stacked plugin-only PR.

## Verification

- `pnpm exec vitest run cli/src/__tests__/data-dir.test.ts
cli/src/__tests__/home-paths.test.ts cli/src/__tests__/onboard.test.ts
packages/shared/src/home-paths.test.ts
packages/db/src/runtime-config.test.ts
server/src/__tests__/agent-instructions-service.test.ts
server/src/__tests__/claude-local-execute.test.ts
server/src/__tests__/codex-local-execute.test.ts`
- `pnpm exec vitest run packages/db/src/runtime-config.test.ts`
- `pnpm exec vitest run
server/src/__tests__/plugin-routes-authz.test.ts`
- `pnpm --filter @paperclipai/server typecheck`
- `pnpm exec vitest run
server/src/__tests__/heartbeat-process-recovery.test.ts -t "reuses the
raced stranded recovery issue"` skipped locally because embedded
Postgres did not initialize on this macOS temp host; the code path was
typechecked and is covered by Linux CI.
- Boundary check: no core references remain for `PAPERCLIP_SPACE_ID`,
`spaces migrate-default`, `@paperclipai/shared/space-paths`,
`registerSpacesCommands`, or the removed bookmarks example.
- Previous PR head `4f23e034` had green GitHub checks: `verify`, all
four serialized server shards, `e2e`, `Canary Dry Run`, `policy`, Snyk,
and `Greptile Review`. Current head `582f466d` is re-running checks
after the bookmarks deletion.

## Risks

- Plugin host changes touch shared runtime paths, so regressions would
most likely appear in adapter startup, plugin loading, or local dev path
defaults.
- Removing the bookmarks example also removes one demonstration of
plugin database namespaces plus local-folder persistence; remaining
plugin examples still cover bundled example discovery and plugin host
flows.
- The plugin package itself is intentionally deferred to the stacked
plugin-only PR, where LLM Wiki plugin-local spaces live.
- Existing installs that tested the transient root-level spaces CLI
should stop using it; this PR intentionally removes that unsupported
migration surface before merge.

> 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 GPT-5 Codex via Codex CLI, tool use and local code execution
enabled; context window not exposed.

## 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
- [x] I have run tests locally and they pass, except where noted above
for host-specific embedded Postgres initialization
- [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

Stacked follow-up: PR #5592 contains only
`packages/plugins/plugin-llm-wiki/` and targets this branch.

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-05-10 07:34:12 -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
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)
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