[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>

packages/plugins/sdk/src/testing.ts

@@ -8,6 +8,8 @@ import type {
   Project,
   Issue,
   IssueComment,
+  IssueThreadInteraction,
+  CreateIssueThreadInteraction,
   IssueDocument,
   Agent,
   Goal,
@@ -149,6 +151,7 @@ export function createTestHarness(options: TestHarnessOptions): TestHarness {
   const issues = new Map<string, Issue>();
   const blockedByIssueIds = new Map<string, string[]>();
   const issueComments = new Map<string, IssueComment[]>();
+  const issueInteractions = new Map<string, IssueThreadInteraction[]>();
   const issueDocuments = new Map<string, IssueDocument>();
   const agents = new Map<string, Agent>();
   const goals = new Map<string, Goal>();
@@ -547,6 +550,50 @@ export function createTestHarness(options: TestHarnessOptions): TestHarness {
         issueComments.set(issueId, current);
         return comment;
       },
+      async createInteraction(issueId, interaction, companyId, options) {
+        requireCapability(manifest, capabilitySet, "issue.interactions.create");
+        const parentIssue = issues.get(issueId);
+        if (!isInCompany(parentIssue, companyId)) {
+          throw new Error(`Issue not found: ${issueId}`);
+        }
+        const now = new Date();
+        const current = issueInteractions.get(issueId) ?? [];
+        if (interaction.idempotencyKey) {
+          const existing = current.find((entry) => entry.idempotencyKey === interaction.idempotencyKey);
+          if (existing) return existing;
+        }
+        const created: IssueThreadInteraction = {
+          id: randomUUID(),
+          companyId: parentIssue.companyId,
+          issueId,
+          kind: interaction.kind,
+          status: "pending",
+          continuationPolicy: interaction.continuationPolicy ?? "wake_assignee",
+          idempotencyKey: interaction.idempotencyKey ?? null,
+          sourceCommentId: interaction.sourceCommentId ?? null,
+          sourceRunId: interaction.sourceRunId ?? null,
+          title: interaction.title ?? null,
+          summary: interaction.summary ?? null,
+          createdByAgentId: options?.authorAgentId ?? null,
+          createdByUserId: null,
+          payload: interaction.payload,
+          result: null,
+          createdAt: now,
+          updatedAt: now,
+        } as IssueThreadInteraction;
+        current.push(created);
+        issueInteractions.set(issueId, current);
+        return created;
+      },
+      async suggestTasks(issueId, interaction, companyId, options) {
+        return this.createInteraction(issueId, { ...interaction, kind: "suggest_tasks" }, companyId, options) as Promise<any>;
+      },
+      async askUserQuestions(issueId, interaction, companyId, options) {
+        return this.createInteraction(issueId, { ...interaction, kind: "ask_user_questions" }, companyId, options) as Promise<any>;
+      },
+      async requestConfirmation(issueId, interaction, companyId, options) {
+        return this.createInteraction(issueId, { ...interaction, kind: "request_confirmation" }, companyId, options) as Promise<any>;
+      },
       documents: {
         async list(issueId, companyId) {
           requireCapability(manifest, capabilitySet, "issue.documents.read");