[codex] Add skills CLI and catalog management (#6782)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies through
company-scoped control-plane workflows.
> - Agents need reusable, inspectable skills that can be installed,
reset, audited, exported, and assigned without bespoke local setup.
> - The existing skill truth model needed cleanup so bundled skills,
optional catalog skills, runtime skills, and adapter-provided skills
have clear provenance.
> - Operators also need a practical CLI and board UI for discovering and
managing company skills.
> - This pull request adds the skills CLI, packaged skills catalog,
company skills APIs, and catalog-aware board UI.
> - The benefit is a more reusable Paperclip company setup where skills
are portable, auditable, and easier for operators and agents to manage.

## What Changed

- Added `paperclipai skills` CLI commands and coverage for catalog
listing, installing, resetting, and inspecting company skills.
- Added a packaged `@paperclipai/skills-catalog` workspace with bundled
and optional skill content plus validation/build tests.
- Added shared company-skill types and validators used across CLI,
server, and UI contracts.
- Added server catalog APIs/services for company skill catalog
operations, reset semantics, audit behavior, and portability provenance.
- Updated adapter skill handling so runtime/catalog provenance remains
explicit across local adapters.
- Added board UI support for browsing and managing catalog-backed
company skills.
- Updated docs for the skills CLI/catalog flow and the company skills
Paperclip skill reference.
- Rebased the branch onto current `paperclipai/paperclip:master`; no
`pnpm-lock.yaml`, `.github/workflows`, or migration files are included
in the final PR diff.

## Verification

- Passed: `pnpm run preflight:workspace-links && pnpm exec vitest run
cli/src/__tests__/skills.test.ts
packages/skills-catalog/src/catalog-builder.test.ts
packages/skills-catalog/src/shipped-catalog.test.ts
packages/shared/src/validators/company-skill.test.ts
packages/adapter-utils/src/server-utils.test.ts
packages/plugins/create-paperclip-plugin/src/entrypoints.test.ts
server/src/__tests__/company-skills-catalog-service.test.ts
server/src/__tests__/company-skills-routes.test.ts
server/src/__tests__/company-portability.test.ts`.
- Passed: `pnpm exec vitest run
server/src/__tests__/workspace-runtime.test.ts -t "default
branch|origin/master|symbolic-ref"`.
- Attempted: full `server/src/__tests__/workspace-runtime.test.ts`. Four
provisioning tests failed while seeding an isolated worktree database
from the local Paperclip instance because the local plugin schema dump
contains a duplicate-column foreign key
(`plugin_content_machine_18a7bc327b.content_case_signals`). The
default-branch tests touched by the rebase conflict passed in the
focused run above.
- Checked final diff: no `pnpm-lock.yaml`, no `.github/workflows`, and
no migration-file changes relative to `master`.

## Risks

- Medium: this is a broad skills/catalog change touching CLI, server
APIs, shared contracts, adapter skill sync, and UI.
- Catalog validation and reset semantics need careful reviewer attention
because they affect reusable company setup and portability.
- No database migrations are included in this PR, so there is no
migration ordering/idempotency risk in the final diff.
- No lockfile is included by design; dependency resolution will be
handled by the repository lockfile workflow.

## Model Used

- OpenAI Codex coding agent based on GPT-5, running in Paperclip via the
`codex_local` adapter with shell, git, GitHub CLI, and code-editing tool
access. Exact hosted model build/context-window metadata is not exposed
in this 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
- [x] I have run targeted tests locally and documented the local
workspace-runtime seed failure above
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, screenshots were intentionally
omitted per PAP-10124 instructions; UI behavior is covered by tests and
reviewer inspection
- [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>

doc/CLI.md

@@ -143,6 +143,124 @@ 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