fix(skills): pull upstream skill runtime resolution to stop event-loop starvation

The fork's listRuntimeSkillEntries rematerialized every skill's files from
the DB on every heartbeat run dispatch — fs.rm + fs.mkdir + per-file
readFile/writeFile, sequentially per skill. With 24 configured skills and
5 concurrent agents, this saturated the Node event loop badly enough that
executeRun continuations couldn't reach activeRunExecutions.add() within
the orphan-reaper's 5-min threshold, causing reaper to false-positive runs
as "process_lost".

Upstream's listRuntimeSkillEntries calls resolveRuntimeSkillSource, which
checks if the materialized directory already exists on disk and short-
circuits when it does. Fixes the symptom at the root.

Replaces these files with upstream/master content:
  - server/src/services/company-skills.ts
  - server/src/services/heartbeat.ts
  - server/src/services/workspace-runtime.ts
  - server/src/services/company-portability.ts
  - server/src/routes/company-skills.ts
  - server/src/routes/agents.ts
  - packages/adapter-utils/src/server-utils.ts

Pulls in supporting upstream files:
  - server/src/services/catalog-provenance.ts
  - server/src/services/skills-catalog.ts
  - server/src/services/github-fetch.ts
  - server/src/services/portable-path.ts
  - packages/skills-catalog/ (new package)
  - packages/db document_annotation_* schema + migration 0091
  - packages/shared document-annotation types/validators

Drops fork features (to be re-evaluated later):
  - Gitea/Forgejo git skill sources (server/src/services/git-source.ts deleted)
  - PAT support for private skill repos
  - Fork-specific secret-export portability extensions

Adds agentId: null to acquireRunLease test-probe call in routes/agents.ts
to satisfy the fork's environment-runtime agentId requirement (kept).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

packages/skills-catalog/src/index.ts

@@ -0,0 +1,37 @@
+import catalogManifestJson from "../generated/catalog.json" with { type: "json" };
+import type { CatalogManifest, CatalogSkill } from "./types.js";
+
+export type {
+  CatalogCompatibility,
+  CatalogManifest,
+  CatalogSkill,
+  CatalogSkillFile,
+  CatalogSkillFileKind,
+  CatalogSkillKind,
+  CatalogTrustLevel,
+  CatalogValidationResult,
+} from "./types.js";
+
+export const catalogManifest = catalogManifestJson as CatalogManifest;
+
+export const catalogSkills: CatalogSkill[] = catalogManifest.skills;
+
+const skillsById = new Map(catalogSkills.map((skill) => [skill.id, skill]));
+const skillsByKey = new Map(catalogSkills.map((skill) => [skill.key, skill]));
+
+export function getCatalogSkill(id: string): CatalogSkill | null {
+  return skillsById.get(id) ?? null;
+}
+
+export function resolveCatalogSkillRef(ref: string): CatalogSkill | null {
+  const normalized = ref.trim();
+  if (normalized.length === 0) return null;
+
+  const exactMatch = skillsById.get(normalized) ?? skillsByKey.get(normalized);
+  if (exactMatch) return exactMatch;
+
+  const slugMatches = catalogSkills.filter((skill) => skill.slug === normalized);
+  if (slugMatches.length === 1) return slugMatches[0]!;
+
+  return null;
+}