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/IssueRelatedWorkPanel.test.tsx

@@ -0,0 +1,96 @@
+import type { ComponentProps } from "react";
+import { renderToStaticMarkup } from "react-dom/server";
+import { describe, expect, it, vi } from "vitest";
+import { IssueRelatedWorkPanel } from "./IssueRelatedWorkPanel";
+
+vi.mock("@/lib/router", () => ({
+  Link: ({ children, to, ...props }: ComponentProps<"a"> & { to: string }) => <a href={to} {...props}>{children}</a>,
+}));
+
+describe("IssueRelatedWorkPanel", () => {
+  it("renders outbound and inbound related work with source labels", () => {
+    const html = renderToStaticMarkup(
+      <IssueRelatedWorkPanel
+        relatedWork={{
+          outbound: [
+            {
+              issue: {
+                id: "issue-2",
+                identifier: "PAP-22",
+                title: "Downstream task",
+                status: "todo",
+                priority: "medium",
+                assigneeAgentId: null,
+                assigneeUserId: null,
+              },
+              mentionCount: 2,
+              sources: [
+                { kind: "title", sourceRecordId: null, label: "title", matchedText: "PAP-22" },
+                { kind: "document", sourceRecordId: "doc-1", label: "plan", matchedText: "/issues/PAP-22" },
+              ],
+            },
+          ],
+          inbound: [
+            {
+              issue: {
+                id: "issue-3",
+                identifier: "PAP-33",
+                title: "Upstream task",
+                status: "in_progress",
+                priority: "high",
+                assigneeAgentId: null,
+                assigneeUserId: null,
+              },
+              mentionCount: 1,
+              sources: [
+                { kind: "comment", sourceRecordId: "comment-1", label: "comment", matchedText: "PAP-1" },
+              ],
+            },
+          ],
+        }}
+      />,
+    );
+
+    expect(html).toContain("References");
+    expect(html).toContain("Referenced by");
+    expect(html).toContain("PAP-22");
+    expect(html).toContain("PAP-33");
+    expect(html).toContain('aria-label="Issue PAP-22: Downstream task"');
+    expect(html).toContain('aria-label="Issue PAP-33: Upstream task"');
+    expect(html).toContain("plan");
+    expect(html).toContain("comment");
+  });
+
+  it("collapses duplicate source labels into a single chip with a count", () => {
+    const html = renderToStaticMarkup(
+      <IssueRelatedWorkPanel
+        relatedWork={{
+          outbound: [],
+          inbound: [
+            {
+              issue: {
+                id: "issue-4",
+                identifier: "PAP-44",
+                title: "Chatty inbound",
+                status: "in_progress",
+                priority: "medium",
+                assigneeAgentId: null,
+                assigneeUserId: null,
+              },
+              mentionCount: 3,
+              sources: [
+                { kind: "comment", sourceRecordId: "c1", label: "comment", matchedText: "PAP-44 first" },
+                { kind: "comment", sourceRecordId: "c2", label: "comment", matchedText: "PAP-44 second" },
+                { kind: "comment", sourceRecordId: "c3", label: "comment", matchedText: "PAP-44 third" },
+              ],
+            },
+          ],
+        }}
+      />,
+    );
+
+    const commentMatches = html.match(/>comment</g) ?? [];
+    expect(commentMatches).toHaveLength(1);
+    expect(html).toContain("×3");
+  });
+});