[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__/adapter-routes.test.ts

@@ -4,6 +4,24 @@ import { afterEach, beforeEach, describe, expect, it } from "vitest";
 import { vi } from "vitest";
 import type { ServerAdapterModule } from "../adapters/index.js";
 
+const mockAdapterPluginStore = vi.hoisted(() => ({
+  listAdapterPlugins: vi.fn(),
+  addAdapterPlugin: vi.fn(),
+  removeAdapterPlugin: vi.fn(),
+  getAdapterPluginByType: vi.fn(),
+  getAdapterPluginsDir: vi.fn(),
+  getDisabledAdapterTypes: vi.fn(),
+  setAdapterDisabled: vi.fn(),
+}));
+
+const mockPluginLoader = vi.hoisted(() => ({
+  buildExternalAdapters: vi.fn(),
+  loadExternalAdapterPackage: vi.fn(),
+  getUiParserSource: vi.fn(),
+  getOrExtractUiParserSource: vi.fn(),
+  reloadExternalAdapter: vi.fn(),
+}));
+
 const overridingConfigSchemaAdapter: ServerAdapterModule = {
   type: "claude_local",
   execute: async () => ({ exitCode: 0, signal: null, timedOut: false }),
@@ -25,12 +43,21 @@ const overridingConfigSchemaAdapter: ServerAdapterModule = {
   }),
 };
 
-let registerServerAdapter: typeof import("../adapters/index.js").registerServerAdapter;
-let unregisterServerAdapter: typeof import("../adapters/index.js").unregisterServerAdapter;
+let registerServerAdapter: typeof import("../adapters/registry.js").registerServerAdapter;
+let unregisterServerAdapter: typeof import("../adapters/registry.js").unregisterServerAdapter;
 let setOverridePaused: typeof import("../adapters/registry.js").setOverridePaused;
 let adapterRoutes: typeof import("../routes/adapters.js").adapterRoutes;
 let errorHandler: typeof import("../middleware/index.js").errorHandler;
 
+function registerModuleMocks() {
+  vi.doMock("node:child_process", async () => vi.importActual("node:child_process"));
+  vi.doMock("../adapters/plugin-loader.js", () => mockPluginLoader);
+  vi.doMock("../services/adapter-plugin-store.js", () => mockAdapterPluginStore);
+  vi.doMock("../routes/adapters.js", async () => vi.importActual("../routes/adapters.js"));
+  vi.doMock("../routes/authz.js", async () => vi.importActual("../routes/authz.js"));
+  vi.doMock("../middleware/index.js", async () => vi.importActual("../middleware/index.js"));
+}
+
 function createApp(actorOverrides: Partial<Express.Request["actor"]> = {}) {
   const app = express();
   app.use(express.json());
@@ -53,18 +80,33 @@ function createApp(actorOverrides: Partial<Express.Request["actor"]> = {}) {
 describe("adapter routes", () => {
   beforeEach(async () => {
     vi.resetModules();
-    vi.doUnmock("../adapters/index.js");
+    vi.doUnmock("node:child_process");
     vi.doUnmock("../adapters/registry.js");
+    vi.doUnmock("../adapters/plugin-loader.js");
+    vi.doUnmock("../services/adapter-plugin-store.js");
     vi.doUnmock("../routes/adapters.js");
+    vi.doUnmock("../routes/authz.js");
     vi.doUnmock("../middleware/index.js");
-    const [adapters, registry, routes, middleware] = await Promise.all([
-      vi.importActual<typeof import("../adapters/index.js")>("../adapters/index.js"),
+    registerModuleMocks();
+    mockAdapterPluginStore.listAdapterPlugins.mockReturnValue([]);
+    mockAdapterPluginStore.addAdapterPlugin.mockResolvedValue(undefined);
+    mockAdapterPluginStore.removeAdapterPlugin.mockReturnValue(false);
+    mockAdapterPluginStore.getAdapterPluginByType.mockReturnValue(undefined);
+    mockAdapterPluginStore.getAdapterPluginsDir.mockReturnValue("/tmp/paperclip-adapter-routes-test");
+    mockAdapterPluginStore.getDisabledAdapterTypes.mockReturnValue([]);
+    mockAdapterPluginStore.setAdapterDisabled.mockReturnValue(false);
+    mockPluginLoader.buildExternalAdapters.mockResolvedValue([]);
+    mockPluginLoader.loadExternalAdapterPackage.mockResolvedValue(null);
+    mockPluginLoader.getUiParserSource.mockResolvedValue(null);
+    mockPluginLoader.getOrExtractUiParserSource.mockResolvedValue(null);
+    mockPluginLoader.reloadExternalAdapter.mockResolvedValue(null);
+    const [registry, routes, middleware] = await Promise.all([
       vi.importActual<typeof import("../adapters/registry.js")>("../adapters/registry.js"),
-      vi.importActual<typeof import("../routes/adapters.js")>("../routes/adapters.js"),
-      vi.importActual<typeof import("../middleware/index.js")>("../middleware/index.js"),
+      import("../routes/adapters.js"),
+      import("../middleware/index.js"),
     ]);
-    registerServerAdapter = adapters.registerServerAdapter;
-    unregisterServerAdapter = adapters.unregisterServerAdapter;
+    registerServerAdapter = registry.registerServerAdapter;
+    unregisterServerAdapter = registry.unregisterServerAdapter;
     setOverridePaused = registry.setOverridePaused;
     adapterRoutes = routes.adapterRoutes;
     errorHandler = middleware.errorHandler;