[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/mcp-server/README.md

@@ -63,6 +63,9 @@ Write tools:
 - `paperclipCheckoutIssue`
 - `paperclipReleaseIssue`
 - `paperclipAddComment`
+- `paperclipSuggestTasks`
+- `paperclipAskUserQuestions`
+- `paperclipRequestConfirmation`
 - `paperclipUpsertIssueDocument`
 - `paperclipRestoreIssueDocumentRevision`
 - `paperclipControlIssueWorkspaceServices`

packages/mcp-server/src/tools.test.ts

@@ -182,6 +182,90 @@ describe("paperclip MCP tools", () => {
     expect(response.content[0]?.text).toContain("http://127.0.0.1:5173");
   });
 
+  it("creates suggest_tasks interactions with the expected issue-scoped payload", async () => {
+    const fetchMock = vi.fn().mockResolvedValue(
+      mockJsonResponse({ id: "interaction-1", kind: "suggest_tasks" }),
+    );
+    vi.stubGlobal("fetch", fetchMock);
+
+    const tool = getTool("paperclipSuggestTasks");
+    await tool.execute({
+      issueId: "PAP-1135",
+      idempotencyKey: "run-1:suggest",
+      payload: {
+        version: 1,
+        tasks: [{ clientKey: "task-1", title: "One" }],
+      },
+    });
+
+    const [url, init] = fetchMock.mock.calls[0] as [string, RequestInit];
+    expect(String(url)).toBe("http://localhost:3100/api/issues/PAP-1135/interactions");
+    expect(init.method).toBe("POST");
+    expect(JSON.parse(String(init.body))).toEqual({
+      kind: "suggest_tasks",
+      continuationPolicy: "wake_assignee",
+      idempotencyKey: "run-1:suggest",
+      payload: {
+        version: 1,
+        tasks: [{ clientKey: "task-1", title: "One" }],
+      },
+    });
+  });
+
+  it("creates request_confirmation interactions with plan target payloads", async () => {
+    const fetchMock = vi.fn().mockResolvedValue(
+      mockJsonResponse({ id: "interaction-1", kind: "request_confirmation" }),
+    );
+    vi.stubGlobal("fetch", fetchMock);
+
+    const tool = getTool("paperclipRequestConfirmation");
+    await tool.execute({
+      issueId: "PAP-1135",
+      idempotencyKey: "confirmation:PAP-1135:plan:33333333-3333-4333-8333-333333333333",
+      title: "Plan approval",
+      payload: {
+        version: 1,
+        prompt: "Accept this plan?",
+        acceptLabel: "Accept plan",
+        allowDeclineReason: true,
+        rejectLabel: "Request changes",
+        rejectRequiresReason: true,
+        supersedeOnUserComment: true,
+        target: {
+          type: "issue_document",
+          key: "plan",
+          revisionId: "33333333-3333-4333-8333-333333333333",
+          revisionNumber: 3,
+        },
+      },
+    });
+
+    const [url, init] = fetchMock.mock.calls[0] as [string, RequestInit];
+    expect(String(url)).toBe("http://localhost:3100/api/issues/PAP-1135/interactions");
+    expect(init.method).toBe("POST");
+    expect(JSON.parse(String(init.body))).toEqual({
+      kind: "request_confirmation",
+      continuationPolicy: "none",
+      idempotencyKey: "confirmation:PAP-1135:plan:33333333-3333-4333-8333-333333333333",
+      title: "Plan approval",
+      payload: {
+        version: 1,
+        prompt: "Accept this plan?",
+        acceptLabel: "Accept plan",
+        allowDeclineReason: true,
+        rejectLabel: "Request changes",
+        rejectRequiresReason: true,
+        supersedeOnUserComment: true,
+        target: {
+          type: "issue_document",
+          key: "plan",
+          revisionId: "33333333-3333-4333-8333-333333333333",
+          revisionNumber: 3,
+        },
+      },
+    });
+  });
+
   it("creates approvals with the expected company-scoped payload", async () => {
     const fetchMock = vi.fn().mockResolvedValue(
       mockJsonResponse({ id: "approval-1" }),

packages/mcp-server/src/tools.ts

@@ -1,9 +1,13 @@
 import { z } from "zod";
 import {
   addIssueCommentSchema,
+  askUserQuestionsPayloadSchema,
   checkoutIssueSchema,
   createApprovalSchema,
   createIssueSchema,
+  issueThreadInteractionContinuationPolicySchema,
+  requestConfirmationPayloadSchema,
+  suggestTasksPayloadSchema,
   updateIssueSchema,
   upsertIssueDocumentSchema,
   linkIssueApprovalSchema,
@@ -107,6 +111,39 @@ const addCommentToolSchema = z.object({
   issueId: issueIdSchema,
 }).merge(addIssueCommentSchema);
 
+const createSuggestTasksToolSchema = z.object({
+  issueId: issueIdSchema,
+  idempotencyKey: z.string().trim().max(255).nullable().optional(),
+  sourceCommentId: z.string().uuid().nullable().optional(),
+  sourceRunId: z.string().uuid().nullable().optional(),
+  title: z.string().trim().max(240).nullable().optional(),
+  summary: z.string().trim().max(1000).nullable().optional(),
+  continuationPolicy: issueThreadInteractionContinuationPolicySchema.optional().default("wake_assignee"),
+  payload: suggestTasksPayloadSchema,
+});
+
+const createAskUserQuestionsToolSchema = z.object({
+  issueId: issueIdSchema,
+  idempotencyKey: z.string().trim().max(255).nullable().optional(),
+  sourceCommentId: z.string().uuid().nullable().optional(),
+  sourceRunId: z.string().uuid().nullable().optional(),
+  title: z.string().trim().max(240).nullable().optional(),
+  summary: z.string().trim().max(1000).nullable().optional(),
+  continuationPolicy: issueThreadInteractionContinuationPolicySchema.optional().default("wake_assignee"),
+  payload: askUserQuestionsPayloadSchema,
+});
+
+const createRequestConfirmationToolSchema = z.object({
+  issueId: issueIdSchema,
+  idempotencyKey: z.string().trim().max(255).nullable().optional(),
+  sourceCommentId: z.string().uuid().nullable().optional(),
+  sourceRunId: z.string().uuid().nullable().optional(),
+  title: z.string().trim().max(240).nullable().optional(),
+  summary: z.string().trim().max(1000).nullable().optional(),
+  continuationPolicy: issueThreadInteractionContinuationPolicySchema.optional().default("none"),
+  payload: requestConfirmationPayloadSchema,
+});
+
 const approvalDecisionSchema = z.object({
   approvalId: approvalIdSchema,
   action: z.enum(["approve", "reject", "requestRevision", "resubmit"]),
@@ -443,6 +480,42 @@ export function createToolDefinitions(client: PaperclipApiClient): ToolDefinitio
       async ({ issueId, ...body }) =>
         client.requestJson("POST", `/issues/${encodeURIComponent(issueId)}/comments`, { body }),
     ),
+    makeTool(
+      "paperclipSuggestTasks",
+      "Create a suggest_tasks interaction on an issue",
+      createSuggestTasksToolSchema,
+      async ({ issueId, ...body }) =>
+        client.requestJson("POST", `/issues/${encodeURIComponent(issueId)}/interactions`, {
+          body: {
+            kind: "suggest_tasks",
+            ...body,
+          },
+        }),
+    ),
+    makeTool(
+      "paperclipAskUserQuestions",
+      "Create an ask_user_questions interaction on an issue",
+      createAskUserQuestionsToolSchema,
+      async ({ issueId, ...body }) =>
+        client.requestJson("POST", `/issues/${encodeURIComponent(issueId)}/interactions`, {
+          body: {
+            kind: "ask_user_questions",
+            ...body,
+          },
+        }),
+    ),
+    makeTool(
+      "paperclipRequestConfirmation",
+      "Create a request_confirmation interaction on an issue",
+      createRequestConfirmationToolSchema,
+      async ({ issueId, ...body }) =>
+        client.requestJson("POST", `/issues/${encodeURIComponent(issueId)}/interactions`, {
+          body: {
+            kind: "request_confirmation",
+            ...body,
+          },
+        }),
+    ),
     makeTool(
       "paperclipUpsertIssueDocument",
       "Create or update an issue document",