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/catalog/bundled/paperclip-operations/issue-triage/SKILL.md

@@ -0,0 +1,74 @@
+---
+name: issue-triage
+description: Triage Paperclip inbox issues that are stale, blocked, in-review, or assigned-but-not-progressing, and decide a single next action per issue (resume, reassign, unblock, escalate, or close).
+key: paperclipai/bundled/paperclip-operations/issue-triage
+recommendedForRoles:
+  - manager
+  - ceo
+  - engineer
+tags:
+  - paperclip
+  - triage
+  - inbox
+  - workflow
+---
+
+# Issue Triage
+
+Convert a noisy inbox into a small set of clear next actions. Each pass through this skill should leave every touched issue with a defined owner, status, and the single concrete action that will move it forward.
+
+## When to use
+
+- Daily or shift-start review of `in_progress`, `in_review`, and `blocked` assignments.
+- An inbox has many open assignments and no clear priority.
+- A manager wants a status read on their reports without asking each agent.
+- You are woken by a comment that suggests an old issue stalled.
+
+## When not to use
+
+- You are checked out on one specific issue and the wake context names it. Work that issue, do not triage the whole inbox.
+- An issue thread already has an open `request_confirmation` or `ask_user_questions`. Wait for the response — re-triage is noise.
+
+## Inputs
+
+- `GET /api/agents/me/inbox-lite` for the compact assignment list.
+- For each candidate issue, `GET /api/issues/{issueId}/heartbeat-context` for compact state including `blockerAttention`, `executionState`, ancestors, and `commentCursor`.
+- Only fall back to the full thread when the heartbeat context is not enough.
+
+## Per-issue triage decision
+
+For each issue, classify into exactly one of:
+
+1. **Resume** — execution path is alive. Confirm the assignee is set and let the heartbeat continue. Do not comment.
+2. **Wake-needed** — assignee is stalled with no live continuation. Post one comment that names the blocker resolution or the exact next action, then leave `in_progress` or move to `todo` so the assignee picks it up.
+3. **Reassign** — the assignee is not the right specialty. Reassign and set `in_review` only if the new assignee is human, otherwise leave `in_progress`.
+4. **Unblock** — a first-class `blockedByIssueIds` entry is now `done` or `cancelled`. If `cancelled`, replace or remove it from `blockedByIssueIds`. The blockers-resolved wake will fire automatically when all are `done`.
+5. **Escalate** — the issue needs board, CTO, or user input. Create a `request_confirmation`, `ask_user_questions`, or `request_board_approval` and set the issue to `in_review`.
+6. **Close** — work is complete, duplicate, or no longer relevant. Set `done` or `cancelled` with a one-line reason.
+
+If you cannot classify in under a minute of reading, escalate rather than guess.
+
+## Stuck-state heuristics
+
+- `in_progress` with no comments or document updates in the last 24h and no monitor or queued continuation → wake-needed.
+- `in_review` with no reviewer participant, no pending interaction, no approval — invalid review path → reassign to a real reviewer or move to `todo`.
+- `blocked` with no `blockedByIssueIds`, only free-text "blocked by X" → convert to first-class blockers or move to `todo` with a named action.
+- `blocked` with all blockers `done` → unblock the issue by setting status back; the assignee will wake.
+- Child issues all complete but parent still `in_progress` → confirm parent acceptance, then close.
+
+## Don't-do list
+
+- Do not @-mention agents during triage; mentions cost budget. Use direct reassignment instead.
+- Do not re-comment on a `blocked` issue if your most recent comment was also a blocked update with no reply since.
+- Do not cancel cross-team issues. Reassign to the responsible manager with a comment.
+- Do not change status without a comment that explains the change.
+
+## Output of a triage pass
+
+A short comment chain or summary message that lists, per issue touched:
+
+- Issue id and title.
+- Verdict (resume / wake-needed / reassign / unblock / escalate / close).
+- The one action you took or asked for.
+
+This is the bar for "the triage is done."