[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>

server/src/services/issue-references.ts

@@ -1,6 +1,13 @@
 import { and, asc, eq, inArray, isNull } from "drizzle-orm";
 import type { Db } from "@paperclipai/db";
-import { documents, issueComments, issueDocuments, issueReferenceMentions, issues } from "@paperclipai/db";
+import {
+  documentAnnotationComments,
+  documents,
+  issueComments,
+  issueDocuments,
+  issueReferenceMentions,
+  issues,
+} from "@paperclipai/db";
 import type {
   IssueReferenceSource,
   IssueReferenceSourceKind,
@@ -230,6 +237,29 @@ export function issueReferenceService(db: Db) {
     }, dbOrTx);
   }
 
+  async function syncAnnotationComment(commentId: string, dbOrTx: any = db) {
+    const comment = await dbOrTx
+      .select({
+        id: documentAnnotationComments.id,
+        companyId: documentAnnotationComments.companyId,
+        issueId: documentAnnotationComments.issueId,
+        body: documentAnnotationComments.body,
+      })
+      .from(documentAnnotationComments)
+      .where(eq(documentAnnotationComments.id, commentId))
+      .then((rows: Array<{ id: string; companyId: string; issueId: string; body: string }>) => rows[0] ?? null);
+    if (!comment) throw notFound("Document annotation comment not found");
+
+    await replaceSourceMentions({
+      companyId: comment.companyId,
+      sourceIssueId: comment.issueId,
+      sourceKind: "comment",
+      sourceRecordId: comment.id,
+      documentKey: null,
+      text: comment.body,
+    }, dbOrTx);
+  }
+
   async function syncDocument(documentId: string, dbOrTx: any = db) {
     const document = await dbOrTx
       .select({
@@ -396,6 +426,7 @@ export function issueReferenceService(db: Db) {
   return {
     syncIssue,
     syncComment,
+    syncAnnotationComment,
     syncDocument,
     deleteDocumentSource,
     syncAllForIssue,