Add first-class issue references (#4214)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies.
> - Operators and agents coordinate through company-scoped issues,
comments, documents, and task relationships.
> - Issue text can mention other tickets, but those references were
previously plain markdown/text without durable relationship data.
> - That made it harder to understand related work, surface backlinks,
and keep cross-ticket context visible in the board.
> - This pull request adds first-class issue reference extraction,
storage, API responses, and UI surfaces.
> - The benefit is that issue references become queryable, navigable,
and visible without relying on ad hoc text scanning.

## What Changed

- Added shared issue-reference parsing utilities and exported
reference-related types/constants.
- Added an `issue_reference_mentions` table, idempotent migration DDL,
schema exports, and database documentation.
- Added server-side issue reference services, route integration,
activity summaries, and a backfill command for existing issue content.
- Added UI reference pills, related-work panels, markdown/editor mention
handling, and issue detail/property rendering updates.
- Added focused shared, server, and UI tests for parsing, persistence,
display, and related-work behavior.
- Rebased `PAP-735-first-class-task-references` cleanly onto
`public-gh/master`; no `pnpm-lock.yaml` changes are included.

## Verification

- `pnpm -r typecheck`
- `pnpm test:run packages/shared/src/issue-references.test.ts
server/src/__tests__/issue-references-service.test.ts
ui/src/components/IssueRelatedWorkPanel.test.tsx
ui/src/components/IssueProperties.test.tsx
ui/src/components/MarkdownBody.test.tsx`

## Risks

- Medium risk because this adds a new issue-reference persistence path
that touches shared parsing, database schema, server routes, and UI
rendering.
- Migration risk is mitigated by `CREATE TABLE IF NOT EXISTS`, guarded
foreign-key creation, and `CREATE INDEX IF NOT EXISTS` statements so
users who have applied an older local version of the numbered migration
can re-run safely.
- UI risk is limited by focused component coverage, but reviewers should
still manually inspect issue detail pages containing ticket references
before merge.

> 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-based coding agent, tool-using shell workflow with
repository inspection, git rebase/push, typecheck, and focused Vitest
verification.

## 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: dotta <dotta@example.com>
Co-authored-by: Paperclip <noreply@paperclip.ing>

ui/src/components/IssueReferencePill.tsx

@@ -0,0 +1,55 @@
+import type { IssueRelationIssueSummary } from "@paperclipai/shared";
+import { Link } from "@/lib/router";
+import { cn } from "../lib/utils";
+import { StatusIcon } from "./StatusIcon";
+
+export function IssueReferencePill({
+  issue,
+  strikethrough,
+  className,
+}: {
+  issue: Pick<IssueRelationIssueSummary, "id" | "identifier" | "title"> &
+    Partial<Pick<IssueRelationIssueSummary, "status">>;
+  strikethrough?: boolean;
+  className?: string;
+}) {
+  const issueLabel = issue.identifier ?? issue.title;
+  const classNames = cn(
+    "paperclip-mention-chip paperclip-mention-chip--issue",
+    "inline-flex items-center gap-1 rounded-full border border-border px-2 py-0.5 text-xs no-underline",
+    issue.identifier && "hover:bg-accent/50 focus-visible:outline-none focus-visible:ring-[3px] focus-visible:ring-ring",
+    strikethrough && "opacity-60 line-through decoration-muted-foreground",
+    className,
+  );
+  const content = (
+    <>
+      {issue.status ? <StatusIcon status={issue.status} className="h-3 w-3 shrink-0" /> : null}
+      <span>{issue.identifier ?? issue.title}</span>
+    </>
+  );
+
+  if (!issue.identifier) {
+    return (
+      <span
+        data-mention-kind="issue"
+        className={classNames}
+        title={issue.title}
+        aria-label={`Issue: ${issue.title}`}
+      >
+        {content}
+      </span>
+    );
+  }
+
+  return (
+    <Link
+      to={`/issues/${issueLabel}`}
+      data-mention-kind="issue"
+      className={classNames}
+      title={issue.title}
+      aria-label={`Issue ${issueLabel}: ${issue.title}`}
+    >
+      {content}
+    </Link>
+  );
+}