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>

server/src/__tests__/issue-comment-reopen-routes.test.ts

@@ -76,6 +76,19 @@ vi.mock("../services/index.js", () => ({
   heartbeatService: () => mockHeartbeatService,
   instanceSettingsService: () => mockInstanceSettingsService,
   issueApprovalService: () => ({}),
+  issueReferenceService: () => ({
+    deleteDocumentSource: async () => undefined,
+    diffIssueReferenceSummary: () => ({
+      addedReferencedIssues: [],
+      removedReferencedIssues: [],
+      currentReferencedIssues: [],
+    }),
+    emptySummary: () => ({ outbound: [], inbound: [] }),
+    listIssueReferenceSummary: async () => ({ outbound: [], inbound: [] }),
+    syncComment: async () => undefined,
+    syncDocument: async () => undefined,
+    syncIssue: async () => undefined,
+  }),
   issueService: () => mockIssueService,
   logActivity: mockLogActivity,
   projectService: () => ({}),
@@ -103,6 +116,19 @@ function registerModuleMocks() {
     heartbeatService: () => mockHeartbeatService,
     instanceSettingsService: () => mockInstanceSettingsService,
     issueApprovalService: () => ({}),
+    issueReferenceService: () => ({
+      deleteDocumentSource: async () => undefined,
+      diffIssueReferenceSummary: () => ({
+        addedReferencedIssues: [],
+        removedReferencedIssues: [],
+        currentReferencedIssues: [],
+      }),
+      emptySummary: () => ({ outbound: [], inbound: [] }),
+      listIssueReferenceSummary: async () => ({ outbound: [], inbound: [] }),
+      syncComment: async () => undefined,
+      syncDocument: async () => undefined,
+      syncIssue: async () => undefined,
+    }),
     issueService: () => mockIssueService,
     logActivity: mockLogActivity,
     projectService: () => ({}),