[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-chat-messages.test.ts

@@ -7,6 +7,7 @@ import {
   type IssueChatComment,
   type IssueChatLinkedRun,
 } from "./issue-chat-messages";
+import type { SuggestTasksInteraction } from "./issue-thread-interactions";
 import type { IssueTimelineEvent } from "./issue-timeline-events";
 import type { LiveRunForIssue } from "../api/heartbeats";
 
@@ -51,6 +52,39 @@ function createComment(overrides: Partial<IssueChatComment> = {}): IssueChatComm
   };
 }
 
+function createInteraction(
+  overrides: Partial<SuggestTasksInteraction> = {},
+): SuggestTasksInteraction {
+  return {
+    id: "interaction-1",
+    companyId: "company-1",
+    issueId: "issue-1",
+    kind: "suggest_tasks",
+    title: "Suggested follow-up work",
+    summary: "Preview the next issue tree before accepting it.",
+    status: "pending",
+    continuationPolicy: "wake_assignee",
+    createdByAgentId: "agent-1",
+    createdByUserId: null,
+    resolvedByAgentId: null,
+    resolvedByUserId: null,
+    createdAt: new Date("2026-04-06T12:02:00.000Z"),
+    updatedAt: new Date("2026-04-06T12:02:00.000Z"),
+    resolvedAt: null,
+    payload: {
+      version: 1,
+      tasks: [
+        {
+          clientKey: "task-1",
+          title: "Prototype the card",
+        },
+      ],
+    },
+    result: null,
+    ...overrides,
+  };
+}
+
 describe("buildAssistantPartsFromTranscript", () => {
   it("maps assistant text, reasoning, and tool activity while omitting noisy stderr", () => {
     const result = buildAssistantPartsFromTranscript([
@@ -343,6 +377,63 @@ describe("buildIssueChatMessages", () => {
     });
   });
 
+  it("merges thread interactions into the same chronological feed as comments and runs", () => {
+    const messages = buildIssueChatMessages({
+      comments: [
+        createComment({
+          id: "comment-1",
+          createdAt: new Date("2026-04-06T12:01:00.000Z"),
+          updatedAt: new Date("2026-04-06T12:01:00.000Z"),
+        }),
+      ],
+      interactions: [
+        createInteraction({
+          id: "interaction-2",
+          createdAt: new Date("2026-04-06T12:02:00.000Z"),
+          updatedAt: new Date("2026-04-06T12:02:00.000Z"),
+        }),
+      ],
+      timelineEvents: [],
+      linkedRuns: [],
+      liveRuns: [
+        {
+          id: "run-live-1",
+          status: "running",
+          invocationSource: "manual",
+          triggerDetail: null,
+          startedAt: "2026-04-06T12:03:00.000Z",
+          finishedAt: null,
+          createdAt: "2026-04-06T12:03:00.000Z",
+          agentId: "agent-1",
+          agentName: "CodexCoder",
+          adapterType: "codex_local",
+        },
+      ],
+      transcriptsByRunId: new Map([
+        [
+          "run-live-1",
+          [{ kind: "assistant", ts: "2026-04-06T12:03:01.000Z", text: "Working on it." }],
+        ],
+      ]),
+      hasOutputForRun: (runId) => runId === "run-live-1",
+      currentUserId: "user-1",
+    });
+
+    expect(messages.map((message) => `${message.role}:${message.id}`)).toEqual([
+      "user:comment-1",
+      "system:interaction:interaction-2",
+      "assistant:run-assistant:run-live-1",
+    ]);
+    expect(messages[1]).toMatchObject({
+      metadata: {
+        custom: {
+          kind: "interaction",
+          anchorId: "interaction-interaction-2",
+        },
+      },
+    });
+  });
+
   it("keeps succeeded runs as assistant messages when transcript output exists", () => {
     const agentMap = new Map<string, Agent>([["agent-1", createAgent("agent-1", "CodexCoder")]]);
     const messages = buildIssueChatMessages({