[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>

ui/src/lib/issue-thread-interactions.ts

@@ -0,0 +1,140 @@
+export type {
+  AskUserQuestionsAnswer,
+  AskUserQuestionsInteraction,
+  AskUserQuestionsPayload,
+  AskUserQuestionsQuestion,
+  AskUserQuestionsQuestionOption,
+  AskUserQuestionsResult,
+  IssueThreadInteraction,
+  IssueThreadInteractionActorFields,
+  IssueThreadInteractionBase,
+  IssueThreadInteractionContinuationPolicy,
+  IssueThreadInteractionStatus,
+  RequestConfirmationInteraction,
+  RequestConfirmationIssueDocumentTarget,
+  RequestConfirmationPayload,
+  RequestConfirmationResult,
+  RequestConfirmationTarget,
+  SuggestedTaskDraft,
+  SuggestTasksInteraction,
+  SuggestTasksPayload,
+  SuggestTasksResult,
+  SuggestTasksResultCreatedTask,
+} from "@paperclipai/shared";
+import type {
+  AskUserQuestionsAnswer,
+  AskUserQuestionsInteraction,
+  AskUserQuestionsQuestion,
+  IssueThreadInteraction,
+  RequestConfirmationInteraction,
+  SuggestedTaskDraft,
+  SuggestTasksInteraction,
+  SuggestTasksResultCreatedTask,
+} from "@paperclipai/shared";
+
+export interface SuggestedTaskTreeNode {
+  task: SuggestedTaskDraft;
+  children: SuggestedTaskTreeNode[];
+}
+
+export function isIssueThreadInteraction(
+  value: unknown,
+): value is IssueThreadInteraction {
+  if (!value || typeof value !== "object") return false;
+  const candidate = value as Partial<IssueThreadInteraction>;
+  return typeof candidate.id === "string"
+    && typeof candidate.companyId === "string"
+    && typeof candidate.issueId === "string"
+    && (
+      candidate.kind === "suggest_tasks"
+      || candidate.kind === "ask_user_questions"
+      || candidate.kind === "request_confirmation"
+    );
+}
+
+export function buildIssueThreadInteractionSummary(
+  interaction: IssueThreadInteraction,
+) {
+  if (interaction.kind === "suggest_tasks") {
+    const count = interaction.payload.tasks.length;
+    if (interaction.status === "accepted") {
+      const createdCount = interaction.result?.createdTasks?.length ?? 0;
+      const skippedCount = interaction.result?.skippedClientKeys?.length ?? 0;
+      if (skippedCount > 0) {
+        return `Accepted ${createdCount} of ${count} tasks`;
+      }
+      return createdCount === 1 ? "Accepted 1 task" : `Accepted ${createdCount} tasks`;
+    }
+    if (interaction.status === "rejected") {
+      return count === 1 ? "Rejected 1 task" : `Rejected ${count} tasks`;
+    }
+    return count === 1 ? "Suggested 1 task" : `Suggested ${count} tasks`;
+  }
+
+  if (interaction.kind === "request_confirmation") {
+    if (interaction.status === "accepted") return "Confirmed request";
+    if (interaction.status === "rejected") return "Declined request";
+    if (interaction.status === "expired") {
+      const outcome = interaction.result?.outcome;
+      if (outcome === "superseded_by_comment") return "Confirmation expired after comment";
+      if (outcome === "stale_target") return "Confirmation expired after target changed";
+      return "Confirmation expired";
+    }
+    return "Requested confirmation";
+  }
+
+  const count = interaction.payload.questions.length;
+  if (interaction.status === "answered") {
+    return count === 1 ? "Answered 1 question" : `Answered ${count} questions`;
+  }
+  return count === 1 ? "Asked 1 question" : `Asked ${count} questions`;
+}
+
+export function buildSuggestedTaskTree(
+  tasks: readonly SuggestedTaskDraft[],
+): SuggestedTaskTreeNode[] {
+  const nodes = new Map<string, SuggestedTaskTreeNode>();
+  for (const task of tasks) {
+    nodes.set(task.clientKey, { task, children: [] });
+  }
+
+  const roots: SuggestedTaskTreeNode[] = [];
+  for (const task of tasks) {
+    const node = nodes.get(task.clientKey);
+    if (!node) continue;
+    const parentNode = task.parentClientKey ? nodes.get(task.parentClientKey) : null;
+    if (parentNode) {
+      parentNode.children.push(node);
+      continue;
+    }
+    roots.push(node);
+  }
+
+  return roots;
+}
+
+export function countSuggestedTaskNodes(node: SuggestedTaskTreeNode): number {
+  return 1 + node.children.reduce((sum, child) => sum + countSuggestedTaskNodes(child), 0);
+}
+
+export function collectSuggestedTaskClientKeys(node: SuggestedTaskTreeNode): string[] {
+  return [
+    node.task.clientKey,
+    ...node.children.flatMap((child) => collectSuggestedTaskClientKeys(child)),
+  ];
+}
+
+export function getQuestionAnswerLabels(args: {
+  question: AskUserQuestionsQuestion;
+  answers: readonly AskUserQuestionsAnswer[];
+}) {
+  const { question, answers } = args;
+  const selectedIds =
+    answers.find((answer) => answer.questionId === question.id)?.optionIds ?? [];
+  const optionLabelById = new Map(
+    question.options.map((option) => [option.id, option.label] as const),
+  );
+  return selectedIds
+    .map((optionId) => optionLabelById.get(optionId))
+    .filter((label): label is string => typeof label === "string");
+}