test: stabilize doctor + pi-embedded suites

src/agents/pi-embedded-runner.run-embedded-pi-agent.appends-new-user-assistant-after-existing-transcript.test.ts

@@ -1,7 +1,7 @@
 import fs from "node:fs/promises";
 import os from "node:os";
 import path from "node:path";
-import { describe, expect, it, vi } from "vitest";
+import { beforeEach, describe, expect, it, vi } from "vitest";
 import type { ClawdbotConfig } from "../config/config.js";
 import { ensureClawdbotModelsJson } from "./models-config.js";
 
@@ -85,9 +85,13 @@ vi.mock("@mariozechner/pi-ai", async () => {
   };
 });
 
-vi.resetModules();
+let runEmbeddedPiAgent: typeof import("./pi-embedded-runner.js").runEmbeddedPiAgent;
 
-const { runEmbeddedPiAgent } = await import("./pi-embedded-runner.js");
+beforeEach(async () => {
+  vi.useRealTimers();
+  vi.resetModules();
+  ({ runEmbeddedPiAgent } = await import("./pi-embedded-runner.js"));
+});
 
 const makeOpenAiConfig = (modelIds: string[]) =>
   ({
@@ -213,7 +217,7 @@ describe("runEmbeddedPiAgent", () => {
     expect(seedAssistantIndex).toBeGreaterThan(seedUserIndex);
     expect(newUserIndex).toBeGreaterThan(seedAssistantIndex);
     expect(newAssistantIndex).toBeGreaterThan(newUserIndex);
-  }, 20_000);
+  }, 45_000);
   it("persists multi-turn user/assistant ordering across runs", async () => {
     const agentDir = await fs.mkdtemp(path.join(os.tmpdir(), "clawdbot-agent-"));
     const workspaceDir = await fs.mkdtemp(path.join(os.tmpdir(), "clawdbot-workspace-"));

src/agents/pi-embedded-runner.run-embedded-pi-agent.writes-models-json-into-provided-agentdir.test.ts

@@ -1,7 +1,7 @@
 import fs from "node:fs/promises";
 import os from "node:os";
 import path from "node:path";
-import { describe, expect, it, vi } from "vitest";
+import { beforeEach, describe, expect, it, vi } from "vitest";
 import type { ClawdbotConfig } from "../config/config.js";
 import { ensureClawdbotModelsJson } from "./models-config.js";
 
@@ -85,9 +85,13 @@ vi.mock("@mariozechner/pi-ai", async () => {
   };
 });
 
-vi.resetModules();
+let runEmbeddedPiAgent: typeof import("./pi-embedded-runner.js").runEmbeddedPiAgent;
 
-const { runEmbeddedPiAgent } = await import("./pi-embedded-runner.js");
+beforeEach(async () => {
+  vi.useRealTimers();
+  vi.resetModules();
+  ({ runEmbeddedPiAgent } = await import("./pi-embedded-runner.js"));
+});
 
 const makeOpenAiConfig = (modelIds: string[]) =>
   ({
@@ -188,7 +192,7 @@ describe("runEmbeddedPiAgent", () => {
 
     await expect(fs.stat(path.join(agentDir, "models.json"))).resolves.toBeTruthy();
   });
-  it("persists the first user message before assistant output", { timeout: 15_000 }, async () => {
+  it("persists the first user message before assistant output", { timeout: 45_000 }, async () => {
     const agentDir = await fs.mkdtemp(path.join(os.tmpdir(), "clawdbot-agent-"));
     const workspaceDir = await fs.mkdtemp(path.join(os.tmpdir(), "clawdbot-workspace-"));
     const sessionFile = path.join(workspaceDir, "session.jsonl");

src/commands/doctor.falls-back-legacy-sandbox-image-missing.test.ts

@@ -248,6 +248,7 @@ vi.mock("../telegram/pairing-store.js", () => ({
 
 vi.mock("../pairing/pairing-store.js", () => ({
   readChannelAllowFromStore: vi.fn().mockResolvedValue([]),
+  upsertChannelPairingRequest: vi.fn().mockResolvedValue({ code: "", created: false }),
 }));
 
 vi.mock("../telegram/token.js", () => ({

src/commands/doctor.migrates-routing-allowfrom-channels-whatsapp-allowfrom.test.ts

@@ -248,6 +248,7 @@ vi.mock("../telegram/pairing-store.js", () => ({
 
 vi.mock("../pairing/pairing-store.js", () => ({
   readChannelAllowFromStore: vi.fn().mockResolvedValue([]),
+  upsertChannelPairingRequest: vi.fn().mockResolvedValue({ code: "", created: false }),
 }));
 
 vi.mock("../telegram/token.js", () => ({

src/commands/doctor.runs-legacy-state-migrations-yes-mode-without.test.ts

@@ -248,6 +248,7 @@ vi.mock("../telegram/pairing-store.js", () => ({
 
 vi.mock("../pairing/pairing-store.js", () => ({
   readChannelAllowFromStore: vi.fn().mockResolvedValue([]),
+  upsertChannelPairingRequest: vi.fn().mockResolvedValue({ code: "", created: false }),
 }));
 
 vi.mock("../telegram/token.js", () => ({

src/commands/doctor.warns-per-agent-sandbox-docker-browser-prune.test.ts

@@ -248,6 +248,7 @@ vi.mock("../telegram/pairing-store.js", () => ({
 
 vi.mock("../pairing/pairing-store.js", () => ({
   readChannelAllowFromStore: vi.fn().mockResolvedValue([]),
+  upsertChannelPairingRequest: vi.fn().mockResolvedValue({ code: "", created: false }),
 }));
 
 vi.mock("../telegram/token.js", () => ({

src/commands/doctor.warns-state-directory-is-missing.test.ts

@@ -248,6 +248,7 @@ vi.mock("../telegram/pairing-store.js", () => ({
 
 vi.mock("../pairing/pairing-store.js", () => ({
   readChannelAllowFromStore: vi.fn().mockResolvedValue([]),
+  upsertChannelPairingRequest: vi.fn().mockResolvedValue({ code: "", created: false }),
 }));
 
 vi.mock("../telegram/token.js", () => ({