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/lib/mention-chips.ts

@@ -1,5 +1,11 @@
 import type { CSSProperties } from "react";
-import { parseAgentMentionHref, parseProjectMentionHref, parseSkillMentionHref, parseUserMentionHref } from "@paperclipai/shared";
+import {
+  parseAgentMentionHref,
+  parseIssueReferenceHref,
+  parseProjectMentionHref,
+  parseSkillMentionHref,
+  parseUserMentionHref,
+} from "@paperclipai/shared";
 import { getAgentIcon } from "./agent-icons";
 import { hexToRgb, pickTextColorForPillBg } from "./color-contrast";
 
@@ -9,6 +15,10 @@ export type ParsedMentionChip =
       agentId: string;
       icon: string | null;
     }
+  | {
+      kind: "issue";
+      identifier: string;
+    }
   | {
       kind: "project";
       projectId: string;
@@ -27,6 +37,14 @@ export type ParsedMentionChip =
 const iconMaskCache = new Map<string, string>();
 
 export function parseMentionChipHref(href: string): ParsedMentionChip | null {
+  const issue = parseIssueReferenceHref(href);
+  if (issue) {
+    return {
+      kind: "issue",
+      identifier: issue.identifier,
+    };
+  }
+
   const agent = parseAgentMentionHref(href);
   if (agent) {
     return {
@@ -111,6 +129,7 @@ export function clearMentionChipDecoration(element: HTMLElement) {
   element.classList.remove(
     "paperclip-mention-chip",
     "paperclip-mention-chip--agent",
+    "paperclip-mention-chip--issue",
     "paperclip-mention-chip--project",
     "paperclip-mention-chip--user",
     "paperclip-mention-chip--skill",