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/IssueProperties.test.tsx

@@ -416,6 +416,126 @@ describe("IssueProperties", () => {
     act(() => root.unmount());
   });
 
+  it("shows related task references below sub-issues", async () => {
+    const root = renderProperties(container, {
+      issue: createIssue({
+        relatedWork: {
+          outbound: [
+            {
+              issue: {
+                id: "issue-22",
+                identifier: "PAP-22",
+                title: "Related task",
+                status: "todo",
+                priority: "medium",
+                assigneeAgentId: null,
+                assigneeUserId: null,
+              },
+              mentionCount: 1,
+              sources: [{ kind: "description", sourceRecordId: null, label: "description", matchedText: "PAP-22" }],
+            },
+          ],
+          inbound: [],
+        },
+      }),
+      childIssues: [],
+      onUpdate: vi.fn(),
+    });
+    await flush();
+
+    expect(container.textContent).not.toContain("Task ids");
+    expect(container.textContent).toContain("Related Tasks");
+    expect(container.textContent).toContain("PAP-22");
+
+    act(() => root.unmount());
+  });
+
+  it("hides related task references already covered by blockers, blocking, and sub-issues", async () => {
+    const root = renderProperties(container, {
+      issue: createIssue({
+        blockedBy: [
+          {
+            id: "issue-22",
+            identifier: "PAP-22",
+            title: "Blocker",
+            status: "todo",
+            priority: "medium",
+            assigneeAgentId: null,
+            assigneeUserId: null,
+          },
+        ],
+        blocks: [
+          {
+            id: "issue-33",
+            identifier: "PAP-33",
+            title: "Blocked issue",
+            status: "todo",
+            priority: "medium",
+            assigneeAgentId: null,
+            assigneeUserId: null,
+          },
+        ],
+        relatedWork: {
+          outbound: [
+            {
+              issue: {
+                id: "issue-22",
+                identifier: "PAP-22",
+                title: "Blocker",
+                status: "todo",
+                priority: "medium",
+                assigneeAgentId: null,
+                assigneeUserId: null,
+              },
+              mentionCount: 1,
+              sources: [{ kind: "description", sourceRecordId: null, label: "description", matchedText: "PAP-22" }],
+            },
+            {
+              issue: {
+                id: "issue-33",
+                identifier: "PAP-33",
+                title: "Blocked issue",
+                status: "todo",
+                priority: "medium",
+                assigneeAgentId: null,
+                assigneeUserId: null,
+              },
+              mentionCount: 1,
+              sources: [{ kind: "description", sourceRecordId: null, label: "description", matchedText: "PAP-33" }],
+            },
+            {
+              issue: {
+                id: "child-44",
+                identifier: "PAP-44",
+                title: "Child issue",
+                status: "todo",
+                priority: "medium",
+                assigneeAgentId: null,
+                assigneeUserId: null,
+              },
+              mentionCount: 1,
+              sources: [{ kind: "description", sourceRecordId: null, label: "description", matchedText: "PAP-44" }],
+            },
+          ],
+          inbound: [],
+        },
+      }),
+      childIssues: [
+        createIssue({
+          id: "child-44",
+          identifier: "PAP-44",
+          title: "Child issue",
+        }),
+      ],
+      onUpdate: vi.fn(),
+    });
+    await flush();
+
+    expect(container.textContent).not.toContain("Related Tasks");
+
+    act(() => root.unmount());
+  });
+
   it("shows an add-label button when labels already exist and opens the picker", async () => {
     const root = renderProperties(container, {
       issue: createIssue({
@@ -531,7 +651,6 @@ describe("IssueProperties", () => {
 
     act(() => rerenderedRoot.unmount());
   });
-
   it("shows a run review action after reviewers are configured and starts execution explicitly when clicked", async () => {
     const onUpdate = vi.fn();
     const root = renderProperties(container, {