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/db/src/schema/document_annotation_anchor_snapshots.ts

@@ -0,0 +1,42 @@
+import type {
+  DocumentAnnotationAnchorConfidence,
+  DocumentAnnotationAnchorSnapshot,
+  DocumentAnnotationAnchorState,
+} from "@paperclipai/shared";
+import { index, integer, jsonb, pgTable, text, timestamp, uuid } from "drizzle-orm/pg-core";
+import { companies } from "./companies.js";
+import { documentAnnotationThreads } from "./document_annotation_threads.js";
+import { documentRevisions } from "./document_revisions.js";
+import { documents } from "./documents.js";
+
+export const documentAnnotationAnchorSnapshots = pgTable(
+  "document_annotation_anchor_snapshots",
+  {
+    id: uuid("id").primaryKey().defaultRandom(),
+    companyId: uuid("company_id").notNull().references(() => companies.id),
+    threadId: uuid("thread_id").notNull().references(() => documentAnnotationThreads.id, { onDelete: "cascade" }),
+    documentId: uuid("document_id").notNull().references(() => documents.id, { onDelete: "cascade" }),
+    fromRevisionId: uuid("from_revision_id").references(() => documentRevisions.id, { onDelete: "set null" }),
+    fromRevisionNumber: integer("from_revision_number"),
+    toRevisionId: uuid("to_revision_id").references(() => documentRevisions.id, { onDelete: "set null" }),
+    toRevisionNumber: integer("to_revision_number").notNull(),
+    previousAnchor: jsonb("previous_anchor").$type<DocumentAnnotationAnchorSnapshot>().notNull(),
+    nextAnchor: jsonb("next_anchor").$type<DocumentAnnotationAnchorSnapshot | null>(),
+    anchorState: text("anchor_state").$type<DocumentAnnotationAnchorState>().notNull(),
+    anchorConfidence: text("anchor_confidence").$type<DocumentAnnotationAnchorConfidence>().notNull(),
+    failureReason: text("failure_reason"),
+    createdAt: timestamp("created_at", { withTimezone: true }).notNull().defaultNow(),
+  },
+  (table) => ({
+    companyThreadCreatedAtIdx: index("document_annotation_anchor_snapshots_company_thread_created_at_idx").on(
+      table.companyId,
+      table.threadId,
+      table.createdAt,
+    ),
+    companyDocumentRevisionIdx: index("document_annotation_anchor_snapshots_company_document_revision_idx").on(
+      table.companyId,
+      table.documentId,
+      table.toRevisionNumber,
+    ),
+  }),
+);

packages/db/src/schema/document_annotation_comments.ts

@@ -0,0 +1,44 @@
+import type { IssueCommentAuthorType } from "@paperclipai/shared";
+import { index, pgTable, text, timestamp, uuid } from "drizzle-orm/pg-core";
+import { agents } from "./agents.js";
+import { companies } from "./companies.js";
+import { documentAnnotationThreads } from "./document_annotation_threads.js";
+import { documents } from "./documents.js";
+import { heartbeatRuns } from "./heartbeat_runs.js";
+import { issues } from "./issues.js";
+
+export const documentAnnotationComments = pgTable(
+  "document_annotation_comments",
+  {
+    id: uuid("id").primaryKey().defaultRandom(),
+    companyId: uuid("company_id").notNull().references(() => companies.id),
+    threadId: uuid("thread_id").notNull().references(() => documentAnnotationThreads.id, { onDelete: "cascade" }),
+    issueId: uuid("issue_id").notNull().references(() => issues.id, { onDelete: "cascade" }),
+    documentId: uuid("document_id").notNull().references(() => documents.id, { onDelete: "cascade" }),
+    body: text("body").notNull(),
+    authorType: text("author_type").$type<IssueCommentAuthorType>().notNull(),
+    authorAgentId: uuid("author_agent_id").references(() => agents.id, { onDelete: "set null" }),
+    authorUserId: text("author_user_id"),
+    createdByRunId: uuid("created_by_run_id").references(() => heartbeatRuns.id, { onDelete: "set null" }),
+    createdAt: timestamp("created_at", { withTimezone: true }).notNull().defaultNow(),
+    updatedAt: timestamp("updated_at", { withTimezone: true }).notNull().defaultNow(),
+  },
+  (table) => ({
+    companyThreadCreatedAtIdx: index("document_annotation_comments_company_thread_created_at_idx").on(
+      table.companyId,
+      table.threadId,
+      table.createdAt,
+    ),
+    companyIssueCreatedAtIdx: index("document_annotation_comments_company_issue_created_at_idx").on(
+      table.companyId,
+      table.issueId,
+      table.createdAt,
+    ),
+    companyDocumentCreatedAtIdx: index("document_annotation_comments_company_document_created_at_idx").on(
+      table.companyId,
+      table.documentId,
+      table.createdAt,
+    ),
+    bodySearchIdx: index("document_annotation_comments_body_search_idx").using("gin", table.body.op("gin_trgm_ops")),
+  }),
+);

packages/db/src/schema/document_annotation_threads.ts

@@ -0,0 +1,70 @@
+import type {
+  DocumentAnnotationAnchorConfidence,
+  DocumentAnnotationAnchorSelector,
+  DocumentAnnotationAnchorState,
+  DocumentAnnotationThreadStatus,
+} from "@paperclipai/shared";
+import { index, integer, jsonb, pgTable, text, timestamp, uuid } from "drizzle-orm/pg-core";
+import { agents } from "./agents.js";
+import { companies } from "./companies.js";
+import { documentRevisions } from "./document_revisions.js";
+import { documents } from "./documents.js";
+import { issues } from "./issues.js";
+
+export const documentAnnotationThreads = pgTable(
+  "document_annotation_threads",
+  {
+    id: uuid("id").primaryKey().defaultRandom(),
+    companyId: uuid("company_id").notNull().references(() => companies.id),
+    issueId: uuid("issue_id").notNull().references(() => issues.id, { onDelete: "cascade" }),
+    documentId: uuid("document_id").notNull().references(() => documents.id, { onDelete: "cascade" }),
+    documentKey: text("document_key").notNull(),
+    status: text("status").$type<DocumentAnnotationThreadStatus>().notNull().default("open"),
+    anchorState: text("anchor_state").$type<DocumentAnnotationAnchorState>().notNull().default("active"),
+    originalRevisionId: uuid("original_revision_id").references(() => documentRevisions.id, { onDelete: "set null" }),
+    originalRevisionNumber: integer("original_revision_number").notNull(),
+    currentRevisionId: uuid("current_revision_id").references(() => documentRevisions.id, { onDelete: "set null" }),
+    currentRevisionNumber: integer("current_revision_number").notNull(),
+    selectedText: text("selected_text").notNull(),
+    prefixText: text("prefix_text").notNull().default(""),
+    suffixText: text("suffix_text").notNull().default(""),
+    normalizedStart: integer("normalized_start").notNull(),
+    normalizedEnd: integer("normalized_end").notNull(),
+    markdownStart: integer("markdown_start").notNull(),
+    markdownEnd: integer("markdown_end").notNull(),
+    anchorConfidence: text("anchor_confidence")
+      .$type<DocumentAnnotationAnchorConfidence>()
+      .notNull()
+      .default("exact"),
+    anchorSelector: jsonb("anchor_selector").$type<DocumentAnnotationAnchorSelector>().notNull(),
+    createdByAgentId: uuid("created_by_agent_id").references(() => agents.id, { onDelete: "set null" }),
+    createdByUserId: text("created_by_user_id"),
+    resolvedByAgentId: uuid("resolved_by_agent_id").references(() => agents.id, { onDelete: "set null" }),
+    resolvedByUserId: text("resolved_by_user_id"),
+    resolvedAt: timestamp("resolved_at", { withTimezone: true }),
+    createdAt: timestamp("created_at", { withTimezone: true }).notNull().defaultNow(),
+    updatedAt: timestamp("updated_at", { withTimezone: true }).notNull().defaultNow(),
+  },
+  (table) => ({
+    companyDocumentStatusIdx: index("document_annotation_threads_company_document_status_idx").on(
+      table.companyId,
+      table.documentId,
+      table.status,
+    ),
+    companyIssueStatusIdx: index("document_annotation_threads_company_issue_status_idx").on(
+      table.companyId,
+      table.issueId,
+      table.status,
+    ),
+    companyCurrentRevisionOpenIdx: index("document_annotation_threads_company_current_revision_open_idx").on(
+      table.companyId,
+      table.documentId,
+      table.currentRevisionId,
+      table.status,
+    ),
+    companyAnchorStateIdx: index("document_annotation_threads_company_anchor_state_idx").on(
+      table.companyId,
+      table.anchorState,
+    ),
+  }),
+);

packages/db/src/schema/index.ts

@@ -55,6 +55,9 @@ export { issueAttachments } from "./issue_attachments.js";
 export { documents } from "./documents.js";
 export { documentRevisions } from "./document_revisions.js";
 export { issueDocuments } from "./issue_documents.js";
+export { documentAnnotationThreads } from "./document_annotation_threads.js";
+export { documentAnnotationComments } from "./document_annotation_comments.js";
+export { documentAnnotationAnchorSnapshots } from "./document_annotation_anchor_snapshots.js";
 export { heartbeatRuns } from "./heartbeat_runs.js";
 export { heartbeatRunEvents } from "./heartbeat_run_events.js";
 export { heartbeatRunWatchdogDecisions } from "./heartbeat_run_watchdog_decisions.js";