[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/adapter-utils/src/server-utils.test.ts

@@ -256,6 +256,11 @@ describe("renderPaperclipWakePrompt", () => {
     expect(DEFAULT_PAPERCLIP_AGENT_PROMPT_TEMPLATE).toContain("do not stop at a plan");
     expect(DEFAULT_PAPERCLIP_AGENT_PROMPT_TEMPLATE).toContain("Use child issues");
     expect(DEFAULT_PAPERCLIP_AGENT_PROMPT_TEMPLATE).toContain("instead of polling agents, sessions, or processes");
+    expect(DEFAULT_PAPERCLIP_AGENT_PROMPT_TEMPLATE).toContain("Create child issues directly when you know what needs to be done");
+    expect(DEFAULT_PAPERCLIP_AGENT_PROMPT_TEMPLATE).toContain("POST /api/issues/{issueId}/interactions");
+    expect(DEFAULT_PAPERCLIP_AGENT_PROMPT_TEMPLATE).toContain("kind suggest_tasks, ask_user_questions, or request_confirmation");
+    expect(DEFAULT_PAPERCLIP_AGENT_PROMPT_TEMPLATE).toContain("confirmation:{issueId}:plan:{revisionId}");
+    expect(DEFAULT_PAPERCLIP_AGENT_PROMPT_TEMPLATE).toContain("Wait for acceptance before creating implementation subtasks");
     expect(DEFAULT_PAPERCLIP_AGENT_PROMPT_TEMPLATE).toContain(
       "Respect budget, pause/cancel, approval gates, and company boundaries",
     );

packages/adapter-utils/src/server-utils.ts

@@ -84,6 +84,9 @@ export const DEFAULT_PAPERCLIP_AGENT_PROMPT_TEMPLATE = [
   "- Leave durable progress in comments, documents, or work products with a clear next action.",
   "- Use child issues for parallel or long delegated work instead of polling agents, sessions, or processes.",
   "- If woken by a human comment on a dependency-blocked issue, respond or triage the comment without treating the blocked deliverable work as unblocked.",
+  "- Create child issues directly when you know what needs to be done; use issue-thread interactions when the board/user must choose suggested tasks, answer structured questions, or confirm a proposal.",
+  "- To ask for that input, create an interaction on the current issue with POST /api/issues/{issueId}/interactions using kind suggest_tasks, ask_user_questions, or request_confirmation. Use continuationPolicy wake_assignee when you need to resume after a response; for request_confirmation this resumes only after acceptance.",
+  "- For plan approval, update the plan document first, then create request_confirmation targeting the latest plan revision with idempotencyKey confirmation:{issueId}:plan:{revisionId}. Wait for acceptance before creating implementation subtasks, and create a fresh confirmation after superseding board/user comments if approval is still needed.",
   "- If blocked, mark the issue blocked and name the unblock owner and action.",
   "- Respect budget, pause/cancel, approval gates, and company boundaries.",
 ].join("\n");