[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>

server/src/services/company-portability.ts

@@ -70,6 +70,12 @@ import { issueService } from "./issues.js";
 import { projectService } from "./projects.js";
 import { routineService } from "./routines.js";
 import { secretService } from "./secrets.js";
+import {
+  PORTABLE_CATALOG_PROVENANCE_STRING_KEYS,
+  readCatalogStringList,
+  readPortableCatalogProvenance,
+} from "./catalog-provenance.js";
+import { normalizePortablePath } from "./portable-path.js";
 
 /** Build OrgNode tree from manifest agent list (slug + reportsToSlug). */
 function buildOrgTreeFromManifest(agents: CompanyPortabilityManifest["agents"]): OrgNode[] {
@@ -228,6 +234,28 @@ function readSkillSourceKind(skill: CompanySkill) {
   return asString(metadata?.sourceKind);
 }
 
+function buildPortableCatalogProvenance(skill: CompanySkill) {
+  if (skill.sourceType !== "catalog") return null;
+  const metadata = isPlainRecord(skill.metadata) ? skill.metadata : null;
+  const provenance: Record<string, unknown> = {
+    skillKey: skill.key,
+  };
+
+  const sourceRef = asString(skill.sourceRef) ?? asString(metadata?.originHash);
+  if (sourceRef) provenance.sourceRef = sourceRef;
+
+  for (const key of PORTABLE_CATALOG_PROVENANCE_STRING_KEYS) {
+    if (key === "sourceRef") continue;
+    const value = asString(metadata?.[key]);
+    if (value) provenance[key] = value;
+  }
+
+  const auditCodes = readCatalogStringList(metadata?.auditCodes);
+  if (auditCodes) provenance.auditCodes = auditCodes;
+
+  return Object.keys(provenance).length > 1 ? provenance : null;
+}
+
 function deriveLocalExportNamespace(skill: CompanySkill, slug: string) {
   const metadata = isPlainRecord(skill.metadata) ? skill.metadata : null;
   const candidates = [
@@ -1415,20 +1443,6 @@ function normalizeInclude(input?: Partial<CompanyPortabilityInclude>): CompanyPo
   };
 }
 
-function normalizePortablePath(input: string) {
-  const normalized = input.replace(/\\/g, "/").replace(/^\.\/+/, "");
-  const parts: string[] = [];
-  for (const segment of normalized.split("/")) {
-    if (!segment || segment === ".") continue;
-    if (segment === "..") {
-      if (parts.length > 0) parts.pop();
-      continue;
-    }
-    parts.push(segment);
-  }
-  return parts.join("/");
-}
-
 function resolvePortablePath(fromPath: string, targetPath: string) {
   const baseDir = path.posix.dirname(fromPath.replace(/\\/g, "/"));
   return normalizePortablePath(path.posix.join(baseDir, targetPath.replace(/\\/g, "/")));
@@ -2126,12 +2140,14 @@ async function withSkillSourceMetadata(skill: CompanySkill, markdown: string) {
   if (sourceEntry) {
     metadata.sources = [...existingSources, sourceEntry];
   }
+  const catalogProvenance = buildPortableCatalogProvenance(skill);
   metadata.skillKey = skill.key;
   metadata.paperclipSkillKey = skill.key;
   metadata.paperclip = {
     ...(isPlainRecord(metadata.paperclip) ? metadata.paperclip : {}),
     skillKey: skill.key,
     slug: skill.slug,
+    ...(catalogProvenance ? { catalog: catalogProvenance } : {}),
   };
   const frontmatter = {
     ...parsed.frontmatter,
@@ -2668,10 +2684,17 @@ function buildManifestFromPackageFiles(
       normalizedMetadata = {
         sourceKind: "url",
       };
-    } else if (metadata) {
-      normalizedMetadata = {
-        sourceKind: "catalog",
-      };
+    } else {
+      const catalogProvenance = readPortableCatalogProvenance(metadata);
+      if (catalogProvenance) {
+        sourceType = "catalog";
+        sourceRef = catalogProvenance.sourceRef;
+        normalizedMetadata = catalogProvenance.metadata;
+      } else if (metadata) {
+        normalizedMetadata = {
+          sourceKind: "catalog",
+        };
+      }
     }
     const key = deriveManifestSkillKey(frontmatter, slug, normalizedMetadata, sourceType, sourceLocator);