[codex] Add structured issue-thread interactions (#4244)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies.
> - Operators supervise that work through issues, comments, approvals,
and the board UI.
> - Some agent proposals need structured board/user decisions, not
hidden markdown conventions or heavyweight governed approvals.
> - Issue-thread interactions already provide a natural thread-native
surface for proposed tasks and questions.
> - This pull request extends that surface with request confirmations,
richer interaction cards, and agent/plugin/MCP helpers.
> - The benefit is that plan approvals and yes/no decisions become
explicit, auditable, and resumable without losing the single-issue
workflow.

## What Changed

- Added persisted issue-thread interactions for suggested tasks,
structured questions, and request confirmations.
- Added board UI cards for interaction review, selection, question
answers, and accept/reject confirmation flows.
- Added MCP and plugin SDK helpers for creating interaction cards from
agents/plugins.
- Updated agent wake instructions, onboarding assets, Paperclip skill
docs, and public docs to prefer structured confirmations for
issue-scoped decisions.
- Rebased the branch onto `public-gh/master` and renumbered branch
migrations to `0063` and `0064`; the idempotency migration uses `ADD
COLUMN IF NOT EXISTS` for old branch users.

## Verification

- `git diff --check public-gh/master..HEAD`
- `pnpm exec vitest run packages/adapter-utils/src/server-utils.test.ts
packages/mcp-server/src/tools.test.ts
packages/shared/src/issue-thread-interactions.test.ts
ui/src/lib/issue-thread-interactions.test.ts
ui/src/lib/issue-chat-messages.test.ts
ui/src/components/IssueThreadInteractionCard.test.tsx
ui/src/components/IssueChatThread.test.tsx
server/src/__tests__/issue-thread-interaction-routes.test.ts
server/src/__tests__/issue-thread-interactions-service.test.ts
server/src/services/issue-thread-interactions.test.ts` -> 9 files / 79
tests passed
- `pnpm -r typecheck` -> passed, including `packages/db` migration
numbering check

## Risks

- Medium: this adds a new issue-thread interaction model across
db/shared/server/ui/plugin surfaces.
- Migration risk is reduced by placing this branch after current master
migrations (`0063`, `0064`) and making the idempotency column add
idempotent for users who applied the old branch numbering.
- UI interaction behavior is covered by component tests, but this PR
does not include browser screenshots.

> 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-class coding agent runtime. Exact model ID and
context window are not exposed in this Paperclip run; tool use and local
shell/code execution were enabled.

## 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
- [ ] 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: Paperclip <noreply@paperclip.ing>

server/src/__tests__/sidebar-preferences-routes.test.ts

@@ -1,8 +1,6 @@
 import express from "express";
 import request from "supertest";
 import { beforeEach, describe, expect, it, vi } from "vitest";
-import { errorHandler } from "../middleware/index.js";
-import { sidebarPreferenceRoutes } from "../routes/sidebar-preferences.js";
 
 const mockSidebarPreferenceService = vi.hoisted(() => ({
   getCompanyOrder: vi.fn(),
@@ -12,12 +10,18 @@ const mockSidebarPreferenceService = vi.hoisted(() => ({
 }));
 const mockLogActivity = vi.hoisted(() => vi.fn());
 
-vi.mock("../services/index.js", () => ({
-  sidebarPreferenceService: () => mockSidebarPreferenceService,
-  logActivity: mockLogActivity,
-}));
+function registerModuleMocks() {
+  vi.doMock("../services/index.js", () => ({
+    sidebarPreferenceService: () => mockSidebarPreferenceService,
+    logActivity: mockLogActivity,
+  }));
+}
 
-function createApp(actor: Record<string, unknown>) {
+async function createApp(actor: Record<string, unknown>) {
+  const [{ sidebarPreferenceRoutes }, { errorHandler }] = await Promise.all([
+    import("../routes/sidebar-preferences.js"),
+    import("../middleware/index.js"),
+  ]);
   const app = express();
   app.use(express.json());
   app.use((req, _res, next) => {
@@ -36,7 +40,13 @@ const ORDERED_IDS = [
 
 describe("sidebar preference routes", () => {
   beforeEach(() => {
-    vi.clearAllMocks();
+    vi.resetModules();
+    vi.doUnmock("../services/index.js");
+    vi.doUnmock("../routes/sidebar-preferences.js");
+    vi.doUnmock("../routes/authz.js");
+    vi.doUnmock("../middleware/index.js");
+    registerModuleMocks();
+    vi.resetAllMocks();
     mockSidebarPreferenceService.getCompanyOrder.mockResolvedValue({
       orderedIds: ORDERED_IDS,
       updatedAt: null,
@@ -56,7 +66,7 @@ describe("sidebar preference routes", () => {
   });
 
   it("returns company rail order for board users", async () => {
-    const app = createApp({
+    const app = await createApp({
       type: "board",
       userId: "user-1",
       source: "session",
@@ -75,7 +85,7 @@ describe("sidebar preference routes", () => {
   });
 
   it("updates company rail order for board users", async () => {
-    const app = createApp({
+    const app = await createApp({
       type: "board",
       userId: "user-1",
       source: "local_implicit",
@@ -92,7 +102,7 @@ describe("sidebar preference routes", () => {
   });
 
   it("returns project order for companies the board user can access", async () => {
-    const app = createApp({
+    const app = await createApp({
       type: "board",
       userId: "user-1",
       source: "session",
@@ -107,7 +117,7 @@ describe("sidebar preference routes", () => {
   });
 
   it("logs project order updates for company-scoped writes", async () => {
-    const app = createApp({
+    const app = await createApp({
       type: "board",
       userId: "user-1",
       source: "session",
@@ -136,7 +146,7 @@ describe("sidebar preference routes", () => {
   });
 
   it("rejects company-scoped reads when the board user lacks company access", async () => {
-    const app = createApp({
+    const app = await createApp({
       type: "board",
       userId: "user-1",
       source: "session",
@@ -151,7 +161,7 @@ describe("sidebar preference routes", () => {
   });
 
   it("rejects agent callers", async () => {
-    const app = createApp({
+    const app = await createApp({
       type: "agent",
       agentId: "agent-1",
       companyId: "company-1",