[codex] Add document annotations and comments (#6733)

## Thinking Path

> - Paperclip orchestrates AI-agent companies through issues, documents,
runs, and durable company-scoped state.
> - Issue documents are where agents and operators capture plans,
handoffs, and work products.
> - Before this change, document collaboration could only happen through
whole-document edits and detached issue comments.
> - Inline document annotations need stable anchors, revision-aware
persistence, and UI affordances that do not break existing document
editing.
> - This pull request adds company-scoped document annotation threads,
comments, anchor snapshots, API routes, and board UI.
> - The benefit is that operators and agents can discuss specific
document passages without losing context as documents evolve.

## What Changed

- Added document annotation tables, schema exports, shared types,
validators, anchor hashing, and text-anchor helpers.
- Added server-side document annotation services and issue routes for
listing, creating, commenting, resolving, and reopening annotation
threads.
- Included annotation summaries in relevant issue document reads and
backup/recovery document workspace behavior.
- Added React UI for inline document highlights, comment panels, mobile
sheet behavior, deep-link focus, and resolved/open filtering.
- Added annotation design artifacts, Storybook coverage, screenshots,
and a screenshot helper script.
- Rebased the branch onto current `paperclipai/paperclip` `master` and
renumbered the annotation migration from `0085_old_swarm` to
`0091_old_swarm`; the SQL uses `IF NOT EXISTS` guards so environments
that previously applied the old migration number can safely apply the
new one.
- Adjusted the new annotation UI tests to use a local async flush helper
because this workspace's React 19.2.4 export does not expose
`React.act`.

## Verification

- `pnpm run preflight:workspace-links && pnpm exec vitest run
packages/shared/src/document-anchors.test.ts
server/src/__tests__/document-annotation-routes.test.ts
server/src/__tests__/document-annotations-service.test.ts
ui/src/components/DocumentAnnotationLayer.test.tsx
ui/src/components/IssueDocumentAnnotations.test.tsx
ui/src/lib/document-annotation-hash.test.ts
ui/src/lib/document-annotation-selection.test.ts`
- Confirmed `git diff --check` passes.
- Confirmed no `pnpm-lock.yaml` or `.github/workflows/*` files are
included in the PR diff.

## Risks

- Medium risk: this adds new persisted annotation tables and routes
across db/shared/server/ui.
- Migration risk is reduced by moving the branch migration to
`0091_old_swarm` after upstream `0090_resource_memberships` and keeping
the SQL idempotent for old `0085_old_swarm` adopters.
- UI risk is mostly around text range anchoring and panel positioning
across long documents, folded content, and mobile layouts; the PR
includes focused unit coverage and design screenshots.

> 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-using software engineering
mode. Context window size is not exposed in this Paperclip runtime.

## 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

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>

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,
+    ),
+  }),
+);