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/package.json

@@ -0,0 +1,49 @@
+{
+  "name": "@paperclipai/skills-catalog",
+  "version": "0.3.1",
+  "license": "MIT",
+  "homepage": "https://github.com/paperclipai/paperclip",
+  "bugs": {
+    "url": "https://github.com/paperclipai/paperclip/issues"
+  },
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/paperclipai/paperclip",
+    "directory": "packages/skills-catalog"
+  },
+  "type": "module",
+  "exports": {
+    ".": "./src/index.ts",
+    "./types": "./src/types.ts",
+    "./catalog.json": "./generated/catalog.json"
+  },
+  "publishConfig": {
+    "access": "public",
+    "exports": {
+      ".": {
+        "types": "./dist/src/index.d.ts",
+        "import": "./dist/src/index.js"
+      },
+      "./types": {
+        "types": "./dist/src/types.d.ts",
+        "import": "./dist/src/types.js"
+      },
+      "./catalog.json": "./dist/generated/catalog.json"
+    },
+    "main": "./dist/src/index.js",
+    "types": "./dist/src/index.d.ts"
+  },
+  "files": [
+    "catalog",
+    "dist",
+    "generated"
+  ],
+  "scripts": {
+    "build": "pnpm run build:manifest && tsc -p tsconfig.json",
+    "build:manifest": "node ../../cli/node_modules/tsx/dist/cli.mjs scripts/build-catalog-manifest.ts",
+    "clean": "rm -rf dist",
+    "test": "pnpm -w exec vitest run --root packages/skills-catalog --config vitest.config.ts",
+    "typecheck": "tsc -p tsconfig.json --noEmit",
+    "validate": "node ../../cli/node_modules/tsx/dist/cli.mjs scripts/validate-catalog.ts"
+  }
+}