[codex] Reject stale company skill refreshes (#4601)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies
> - Company skills are part of the reusable agent capability layer
> - Skill inventory refresh work can outlive the company it was
requested for
> - Without an explicit company existence check, stale refreshes can
continue into bundled/local skill cleanup for deleted or missing
companies
> - This pull request makes company-skill listing fail fast when the
company no longer exists
> - The benefit is clearer API behavior and less stale background work
against missing company scope

## What Changed

- Added a company existence check before `companySkillService.list()`
refreshes bundled and local-path skill state.
- Added regression coverage asserting missing companies return `404
Company not found`.

## Verification

- `pnpm exec vitest run --project @paperclipai/server
server/src/__tests__/company-skills-service.test.ts --pool=forks
--poolOptions.forks.isolate=true` exits 0, but this host skipped the
embedded Postgres tests with the existing init guard.

## Risks

- Low risk. Existing callers for valid companies are unchanged.
- Missing-company callers now receive an explicit 404 instead of
continuing refresh work.

> 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, tool-enabled terminal/GitHub
workflow, reasoning mode active. Context window not exposed in this
environment.

## 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
- [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

server/src/__tests__/company-skills-service.test.ts

@@ -89,4 +89,11 @@ describeEmbeddedPostgres("companySkillService.list", () => {
       editable: true,
     });
   });
+
+  it("rejects skill inventory refresh for a missing company", async () => {
+    await expect(svc.list(randomUUID())).rejects.toMatchObject({
+      status: 404,
+      message: "Company not found",
+    });
+  });
 });

server/src/services/company-skills.ts

@@ -4,7 +4,7 @@ import path from "node:path";
 import { fileURLToPath } from "node:url";
 import { and, asc, eq } from "drizzle-orm";
 import type { Db } from "@paperclipai/db";
-import { companySkills } from "@paperclipai/db";
+import { companies, companySkills } from "@paperclipai/db";
 import { readPaperclipSkillSyncPreference } from "@paperclipai/adapter-utils/server-utils";
 import type { PaperclipSkillEntry } from "@paperclipai/adapter-utils/server-utils";
 import type {
@@ -1610,6 +1610,14 @@ export function companySkillService(db: Db) {
     }
 
     const refreshPromise = (async () => {
+      const companyExists = await db
+        .select({ id: companies.id })
+        .from(companies)
+        .where(eq(companies.id, companyId))
+        .then((rows) => rows.length > 0);
+      if (!companyExists) {
+        throw notFound("Company not found");
+      }
       await ensureBundledSkills(companyId);
       await pruneMissingLocalPathSkills(companyId);
     })();