[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>

ui/src/api/companySkills.ts

@@ -1,9 +1,14 @@
 import type {
+  CatalogSkill,
+  CatalogSkillFileDetail,
+  CatalogSkillKind,
   CompanySkill,
   CompanySkillCreateRequest,
   CompanySkillDetail,
   CompanySkillFileDetail,
   CompanySkillImportResult,
+  CompanySkillInstallCatalogRequest,
+  CompanySkillInstallCatalogResult,
   CompanySkillListItem,
   CompanySkillProjectScanRequest,
   CompanySkillProjectScanResult,
@@ -11,6 +16,12 @@ import type {
 } from "@paperclipai/shared";
 import { api } from "./client";
 
+export interface CatalogListQuery {
+  kind?: CatalogSkillKind;
+  category?: string;
+  q?: string;
+}
+
 export const companySkillsApi = {
   list: (companyId: string) =>
     api.get<CompanySkillListItem[]>(`/companies/${encodeURIComponent(companyId)}/skills`),
@@ -55,4 +66,23 @@ export const companySkillsApi = {
     api.delete<CompanySkill>(
       `/companies/${encodeURIComponent(companyId)}/skills/${encodeURIComponent(skillId)}`,
     ),
+  catalogList: (query: CatalogListQuery = {}) => {
+    const params = new URLSearchParams();
+    if (query.kind) params.set("kind", query.kind);
+    if (query.category) params.set("category", query.category);
+    if (query.q) params.set("q", query.q);
+    const search = params.toString();
+    return api.get<CatalogSkill[]>(`/skills/catalog${search ? `?${search}` : ""}`);
+  },
+  catalogDetail: (catalogRef: string) =>
+    api.get<CatalogSkill>(`/skills/catalog/${encodeURIComponent(catalogRef)}`),
+  catalogFile: (catalogRef: string, relativePath: string = "SKILL.md") =>
+    api.get<CatalogSkillFileDetail>(
+      `/skills/catalog/${encodeURIComponent(catalogRef)}/files?path=${encodeURIComponent(relativePath)}`,
+    ),
+  installCatalog: (companyId: string, payload: CompanySkillInstallCatalogRequest) =>
+    api.post<CompanySkillInstallCatalogResult>(
+      `/companies/${encodeURIComponent(companyId)}/skills/install-catalog`,
+      payload,
+    ),
 };

ui/src/lib/queryKeys.ts

@@ -11,6 +11,11 @@ export const queryKeys = {
       ["company-skills", companyId, skillId, "update-status"] as const,
     file: (companyId: string, skillId: string, relativePath: string) =>
       ["company-skills", companyId, skillId, "file", relativePath] as const,
+    catalog: (filters: { kind?: string; category?: string; q?: string } = {}) =>
+      ["company-skills", "catalog", filters.kind ?? "__all-kinds__", filters.category ?? "__all-categories__", filters.q ?? ""] as const,
+    catalogDetail: (catalogRef: string) => ["company-skills", "catalog", "detail", catalogRef] as const,
+    catalogFile: (catalogRef: string, relativePath: string) =>
+      ["company-skills", "catalog", "file", catalogRef, relativePath] as const,
   },
   agents: {
     list: (companyId: string) => ["agents", companyId] as const,

ui/src/pages/AgentDetail.tsx

@@ -2801,6 +2801,14 @@ export function AgentSkillsTab({
         })),
     [companySkillKeys, skillSnapshot],
   );
+  const installedSkillRows = useMemo(
+    () => optionalSkillRows.filter((skill) => skillDraft.includes(skill.key)),
+    [optionalSkillRows, skillDraft],
+  );
+  const otherSkillRows = useMemo(
+    () => optionalSkillRows.filter((skill) => !skillDraft.includes(skill.key)),
+    [optionalSkillRows, skillDraft],
+  );
   const desiredOnlyMissingSkills = useMemo(
     () => skillDraft.filter((key) => !companySkillByKey.has(key)),
     [companySkillByKey, skillDraft],
@@ -2965,6 +2973,30 @@ export function AgentSkillsTab({
               );
             };
 
+            const renderSkillSection = (
+              title: string,
+              rows: SkillRow[],
+              emptyMessage?: string,
+            ) => {
+              if (rows.length === 0 && !emptyMessage) return null;
+              return (
+                <section className="border-y border-border">
+                  <div className="border-b border-border bg-muted/40 px-3 py-2">
+                    <span className="text-xs font-medium text-muted-foreground">
+                      {title}
+                    </span>
+                  </div>
+                  {rows.length > 0 ? (
+                    rows.map(renderSkillRow)
+                  ) : (
+                    <div className="px-3 py-3 text-sm text-muted-foreground">
+                      {emptyMessage}
+                    </div>
+                  )}
+                </section>
+              );
+            };
+
             if (optionalSkillRows.length === 0 && requiredSkillRows.length === 0 && unmanagedSkillRows.length === 0) {
               return (
                 <section className="border-y border-border">
@@ -2977,22 +3009,17 @@ export function AgentSkillsTab({
 
             return (
               <>
-                {optionalSkillRows.length > 0 && (
-                  <section className="border-y border-border">
-                    {optionalSkillRows.map(renderSkillRow)}
-                  </section>
-                )}
+                {optionalSkillRows.length > 0
+                  ? renderSkillSection(
+                      "Installed skills",
+                      installedSkillRows,
+                      "No company-library skills installed on this agent.",
+                    )
+                  : null}
 
-                {requiredSkillRows.length > 0 && (
-                  <section className="border-y border-border">
-                    <div className="border-b border-border bg-muted/40 px-3 py-2">
-                      <span className="text-xs font-medium text-muted-foreground">
-                        Required by Paperclip
-                      </span>
-                    </div>
-                    {requiredSkillRows.map(renderSkillRow)}
-                  </section>
-                )}
+                {renderSkillSection("Other skills", otherSkillRows)}
+
+                {renderSkillSection("Required by Paperclip", requiredSkillRows)}
 
                 {unmanagedSkillRows.length > 0 && (
                   <section className="border-y border-border">