[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__/issue-comment-reopen-routes.test.ts

@@ -57,44 +57,9 @@ const mockInstanceSettingsService = vi.hoisted(() => ({
 const mockRoutineService = vi.hoisted(() => ({
   syncRunStatusForIssue: vi.fn(async () => undefined),
 }));
-
-vi.mock("@paperclipai/shared/telemetry", () => ({
-  trackAgentTaskCompleted: vi.fn(),
-  trackErrorHandlerCrash: vi.fn(),
-}));
-
-vi.mock("../telemetry.js", () => ({
-  getTelemetryClient: vi.fn(() => ({ track: vi.fn() })),
-}));
-
-vi.mock("../services/index.js", () => ({
-  accessService: () => mockAccessService,
-  agentService: () => mockAgentService,
-  documentService: () => ({}),
-  executionWorkspaceService: () => ({}),
-  feedbackService: () => mockFeedbackService,
-  goalService: () => ({}),
-  heartbeatService: () => mockHeartbeatService,
-  instanceSettingsService: () => mockInstanceSettingsService,
-  issueApprovalService: () => ({}),
-  issueReferenceService: () => ({
-    deleteDocumentSource: async () => undefined,
-    diffIssueReferenceSummary: () => ({
-      addedReferencedIssues: [],
-      removedReferencedIssues: [],
-      currentReferencedIssues: [],
-    }),
-    emptySummary: () => ({ outbound: [], inbound: [] }),
-    listIssueReferenceSummary: async () => ({ outbound: [], inbound: [] }),
-    syncComment: async () => undefined,
-    syncDocument: async () => undefined,
-    syncIssue: async () => undefined,
-  }),
-  issueService: () => mockIssueService,
-  logActivity: mockLogActivity,
-  projectService: () => ({}),
-  routineService: () => mockRoutineService,
-  workProductService: () => ({}),
+const mockIssueThreadInteractionService = vi.hoisted(() => ({
+  expireRequestConfirmationsSupersededByComment: vi.fn(async () => []),
+  expireStaleRequestConfirmationsForIssueDocument: vi.fn(async () => []),
 }));
 
 function registerModuleMocks() {
@@ -107,6 +72,38 @@ function registerModuleMocks() {
     getTelemetryClient: vi.fn(() => ({ track: vi.fn() })),
   }));
 
+  vi.doMock("../services/access.js", () => ({
+    accessService: () => mockAccessService,
+  }));
+
+  vi.doMock("../services/activity-log.js", () => ({
+    logActivity: mockLogActivity,
+  }));
+
+  vi.doMock("../services/agents.js", () => ({
+    agentService: () => mockAgentService,
+  }));
+
+  vi.doMock("../services/feedback.js", () => ({
+    feedbackService: () => mockFeedbackService,
+  }));
+
+  vi.doMock("../services/heartbeat.js", () => ({
+    heartbeatService: () => mockHeartbeatService,
+  }));
+
+  vi.doMock("../services/instance-settings.js", () => ({
+    instanceSettingsService: () => mockInstanceSettingsService,
+  }));
+
+  vi.doMock("../services/issues.js", () => ({
+    issueService: () => mockIssueService,
+  }));
+
+  vi.doMock("../services/routines.js", () => ({
+    routineService: () => mockRoutineService,
+  }));
+
   vi.doMock("../services/index.js", () => ({
     accessService: () => mockAccessService,
     agentService: () => mockAgentService,
@@ -131,6 +128,7 @@ function registerModuleMocks() {
       syncIssue: async () => undefined,
     }),
     issueService: () => mockIssueService,
+    issueThreadInteractionService: () => mockIssueThreadInteractionService,
     logActivity: mockLogActivity,
     projectService: () => ({}),
     routineService: () => mockRoutineService,
@@ -191,6 +189,17 @@ function makeIssue(status: "todo" | "done" | "blocked") {
 describe("issue comment reopen routes", () => {
   beforeEach(() => {
     vi.resetModules();
+    vi.doUnmock("@paperclipai/shared/telemetry");
+    vi.doUnmock("../telemetry.js");
+    vi.doUnmock("../services/access.js");
+    vi.doUnmock("../services/activity-log.js");
+    vi.doUnmock("../services/agents.js");
+    vi.doUnmock("../services/feedback.js");
+    vi.doUnmock("../services/heartbeat.js");
+    vi.doUnmock("../services/index.js");
+    vi.doUnmock("../services/instance-settings.js");
+    vi.doUnmock("../services/issues.js");
+    vi.doUnmock("../services/routines.js");
     vi.doUnmock("../routes/issues.js");
     vi.doUnmock("../routes/authz.js");
     vi.doUnmock("../middleware/index.js");
@@ -789,26 +798,20 @@ describe("issue comment reopen routes", () => {
       });
 
     expect(res.status).toBe(200);
-    expect(mockIssueService.update).toHaveBeenCalledWith(
-      "11111111-1111-4111-8111-111111111111",
-      expect.objectContaining({
-        status: "in_review",
-        assigneeAgentId: "33333333-3333-4333-8333-333333333333",
-        assigneeUserId: null,
-        executionState: expect.objectContaining({
-          status: "pending",
-          currentStageType: "review",
-          currentParticipant: expect.objectContaining({
-            type: "agent",
-            agentId: "33333333-3333-4333-8333-333333333333",
-          }),
-          returnAssignee: expect.objectContaining({
-            type: "agent",
-            agentId: "22222222-2222-4222-8222-222222222222",
-          }),
-        }),
-      }),
-    );
+    expect(res.body.assigneeAgentId).toBe("33333333-3333-4333-8333-333333333333");
+    expect(res.body.assigneeUserId).toBeNull();
+    expect(res.body.executionState).toMatchObject({
+      status: "pending",
+      currentStageType: "review",
+      currentParticipant: {
+        type: "agent",
+        agentId: "33333333-3333-4333-8333-333333333333",
+      },
+      returnAssignee: {
+        type: "agent",
+        agentId: "22222222-2222-4222-8222-222222222222",
+      },
+    });
     expect(mockHeartbeatService.wakeup).toHaveBeenCalledWith(
       "33333333-3333-4333-8333-333333333333",
       expect.objectContaining({