test(cli): update all CLI command tests

Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)

Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>

src/cli/config-manager/bun-install.test.ts

@@ -2,13 +2,14 @@
 
 import * as fs from "node:fs"
 
-import { afterEach, beforeEach, describe, expect, it, jest, spyOn } from "bun:test"
+import { afterEach, beforeEach, describe, expect, it, spyOn } from "bun:test"
 
 import * as dataPath from "../../shared/data-path"
 import * as logger from "../../shared/logger"
 import * as spawnHelpers from "../../shared/spawn-with-windows-hide"
 import type { BunInstallResult } from "./bun-install"
-import { runBunInstallWithDetails } from "./bun-install"
+
+type BunInstallModule = typeof import("./bun-install")
 
 type CreateProcOptions = {
   exitCode?: number | null
@@ -37,12 +38,16 @@ describe("runBunInstallWithDetails", () => {
   let logSpy: ReturnType<typeof spyOn>
   let spawnWithWindowsHideSpy: ReturnType<typeof spyOn>
   let existsSyncSpy: ReturnType<typeof spyOn>
+  let runBunInstallWithDetails: BunInstallModule["runBunInstallWithDetails"]
 
-  beforeEach(() => {
+  beforeEach(async () => {
     getOpenCodeCacheDirSpy = spyOn(dataPath, "getOpenCodeCacheDir").mockReturnValue("/tmp/opencode-cache")
     logSpy = spyOn(logger, "log").mockImplementation(() => {})
     spawnWithWindowsHideSpy = spyOn(spawnHelpers, "spawnWithWindowsHide").mockReturnValue(createProc())
     existsSyncSpy = spyOn(fs, "existsSync").mockReturnValue(true)
+
+    const bunInstallModule = await import(`./bun-install?test=${Date.now()}-${Math.random()}`)
+    runBunInstallWithDetails = bunInstallModule.runBunInstallWithDetails
   })
 
   afterEach(() => {
@@ -136,9 +141,30 @@ describe("runBunInstallWithDetails", () => {
     describe("#when the install times out and proc.exited never resolves", () => {
       it("#then returns timedOut true without hanging", async () => {
         // given
-        jest.useFakeTimers()
-
         let killCallCount = 0
+        const originalSetTimeout = globalThis.setTimeout
+        const originalClearTimeout = globalThis.clearTimeout
+
+        Object.defineProperty(globalThis, "setTimeout", {
+          configurable: true,
+          value: Object.assign(
+            (callback: TimerHandler) => {
+              if (typeof callback === "function") {
+                callback()
+              }
+
+              return 0
+            },
+            {
+              __promisify__: originalSetTimeout.__promisify__,
+            }
+          ),
+        })
+        Object.defineProperty(globalThis, "clearTimeout", {
+          configurable: true,
+          value: () => undefined,
+        })
+
         spawnWithWindowsHideSpy.mockReturnValue(
           createProc({
             exitCode: null,
@@ -148,38 +174,28 @@ describe("runBunInstallWithDetails", () => {
             },
           })
         )
+        const timeoutAwareModule = await import(`./bun-install?timeout-test=${Date.now()}-${Math.random()}`)
 
         try {
           // when
-          const resultPromise = runBunInstallWithDetails({ outputMode: "pipe" })
+          const outcome = await timeoutAwareModule.runBunInstallWithDetails({ outputMode: "pipe" })
-          jest.advanceTimersByTime(60_000)
-          jest.runOnlyPendingTimers()
-          await Promise.resolve()
-
-          const outcome = await Promise.race([
-            resultPromise.then((result) => ({
-              status: "resolved" as const,
-              result,
-            })),
-            new Promise<{ status: "pending" }>((resolve) => {
-              queueMicrotask(() => resolve({ status: "pending" }))
-            }),
-          ])
 
           // then
-          if (outcome.status === "pending") {
+          expect(outcome).toEqual({
-            throw new Error("runBunInstallWithDetails did not resolve after timing out")
-          }
-
-          expect(outcome.result).toEqual({
             success: false,
             timedOut: true,
             error: 'bun install timed out after 60 seconds. Try running manually: cd "/tmp/opencode-cache/packages" && bun i',
           } satisfies BunInstallResult)
           expect(killCallCount).toBe(1)
         } finally {
-          jest.clearAllTimers()
+          Object.defineProperty(globalThis, "setTimeout", {
-          jest.useRealTimers()
+            configurable: true,
+            value: originalSetTimeout,
+          })
+          Object.defineProperty(globalThis, "clearTimeout", {
+            configurable: true,
+            value: originalClearTimeout,
+          })
         }
       })
     })

src/cli/doctor/checks/system.test.ts

@@ -1,12 +1,15 @@
 /// <reference types="bun-types" />
 
-import { afterAll, beforeEach, describe, expect, it, mock } from "bun:test"
+import { beforeEach, describe, expect, it, mock } from "bun:test"
 import { PLUGIN_NAME } from "../../../shared"
 import type { PluginInfo } from "./system-plugin"
+import type { OpenCodeBinaryInfo } from "./system-binary"
+import { checkSystem } from "./system"
 
-type SystemModule = typeof import("./system")
+const mockFindOpenCodeBinary = mock<() => Promise<OpenCodeBinaryInfo | null>>(async () => ({
-
+  binary: "opencode",
-const mockFindOpenCodeBinary = mock(async () => ({ path: "/usr/local/bin/opencode" }))
+  path: "/usr/local/bin/opencode",
+}))
 const mockGetOpenCodeVersion = mock(async () => "1.0.200")
 const mockCompareVersions = mock((_leftVersion?: string, _rightVersion?: string) => true)
 const mockGetPluginInfo = mock((): PluginInfo => ({
@@ -27,35 +30,17 @@ const mockGetLoadedPluginVersion = mock(() => ({
 const mockGetLatestPluginVersion = mock(async (_currentVersion: string | null) => null as string | null)
 const mockGetSuggestedInstallTag = mock(() => "latest")
 
-const realSystemBinary = require("./system-binary")
-const realSystemPlugin = require("./system-plugin")
-const realSystemLoadedVersion = require("./system-loaded-version")
 
-afterAll(() => {
+function createSystemDeps() {
-  mock.module("./system-binary", () => realSystemBinary)
+  return {
-  mock.module("./system-plugin", () => realSystemPlugin)
-  mock.module("./system-loaded-version", () => realSystemLoadedVersion)
-  mock.restore()
-})
-
-async function importFreshSystemModule(): Promise<SystemModule> {
-  mock.module("./system-binary", () => ({
     findOpenCodeBinary: mockFindOpenCodeBinary,
     getOpenCodeVersion: mockGetOpenCodeVersion,
     compareVersions: mockCompareVersions,
-  }))
-
-  mock.module("./system-plugin", () => ({
     getPluginInfo: mockGetPluginInfo,
-  }))
-
-  mock.module("./system-loaded-version", () => ({
     getLoadedPluginVersion: mockGetLoadedPluginVersion,
     getLatestPluginVersion: mockGetLatestPluginVersion,
     getSuggestedInstallTag: mockGetSuggestedInstallTag,
-  }))
+  }
-
-  return import(`./system?test=${Date.now()}-${Math.random()}`)
 }
 
 describe("system check", () => {
@@ -68,7 +53,10 @@ describe("system check", () => {
     mockGetLatestPluginVersion.mockReset()
     mockGetSuggestedInstallTag.mockReset()
 
-    mockFindOpenCodeBinary.mockResolvedValue({ path: "/usr/local/bin/opencode" })
+    mockFindOpenCodeBinary.mockResolvedValue({
+      binary: "opencode",
+      path: "/usr/local/bin/opencode",
+    })
     mockGetOpenCodeVersion.mockResolvedValue("1.0.200")
     mockCompareVersions.mockReturnValue(true)
     mockGetPluginInfo.mockReturnValue({
@@ -93,10 +81,8 @@ describe("system check", () => {
   describe("#given cache directory contains spaces", () => {
     it("uses a quoted cache directory in mismatch fix command", async () => {
       //#given
-      const { checkSystem } = await importFreshSystemModule()
-
       //#when
-      const result = await checkSystem()
+      const result = await checkSystem(createSystemDeps())
 
       //#then
       const mismatchIssue = result.issues.find((issue) => issue.title === "Loaded plugin version mismatch")
@@ -114,13 +100,12 @@ describe("system check", () => {
       })
       mockGetLatestPluginVersion.mockResolvedValue("3.0.0-canary.2")
       mockGetSuggestedInstallTag.mockReturnValue("canary")
-      mockCompareVersions.mockImplementation((leftVersion?: string, rightVersion?: string) => {
+      mockCompareVersions
-        return !(leftVersion === "3.0.0-canary.1" && rightVersion === "3.0.0-canary.2")
+        .mockImplementationOnce(() => true)
-      })
+        .mockImplementationOnce(() => false)
-      const { checkSystem } = await importFreshSystemModule()
 
       //#when
-      const result = await checkSystem()
+      const result = await checkSystem(createSystemDeps())
 
       //#then
       const outdatedIssue = result.issues.find((issue) => issue.title === "Loaded plugin is outdated")
@@ -141,10 +126,9 @@ describe("system check", () => {
         configPath: null,
         isLocalDev: false,
       })
-      const { checkSystem } = await importFreshSystemModule()
 
       //#when
-      const result = await checkSystem()
+      const result = await checkSystem(createSystemDeps())
 
       //#then
       const legacyEntryIssue = result.issues.find((issue) => issue.title === "Using legacy package name")
@@ -164,10 +148,9 @@ describe("system check", () => {
         configPath: null,
         isLocalDev: false,
       })
-      const { checkSystem } = await importFreshSystemModule()
 
       //#when
-      const result = await checkSystem()
+      const result = await checkSystem(createSystemDeps())
 
       //#then
       const legacyEntryIssue = result.issues.find((issue) => issue.title === "Using legacy package name")
@@ -187,10 +170,9 @@ describe("system check", () => {
         configPath: null,
         isLocalDev: false,
       })
-      const { checkSystem } = await importFreshSystemModule()
 
       //#when
-      const result = await checkSystem()
+      const result = await checkSystem(createSystemDeps())
 
       //#then
       expect(result.issues.some((issue) => issue.title === "Using legacy package name")).toBe(false)
@@ -206,10 +188,9 @@ describe("system check", () => {
         configPath: null,
         isLocalDev: true,
       })
-      const { checkSystem } = await importFreshSystemModule()
 
       //#when
-      const result = await checkSystem()
+      const result = await checkSystem(createSystemDeps())
 
       //#then
       expect(result.issues.some((issue) => issue.title === "Using legacy package name")).toBe(false)

src/cli/run/continuation-state.json-backend.test.ts

@@ -8,6 +8,7 @@ const testDirs: string[] = []
 
 const TEST_STORAGE_ROOT = join(tmpdir(), `omo-run-json-storage-${Date.now()}`)
 const TEST_MESSAGE_STORAGE = join(TEST_STORAGE_ROOT, "message")
+const sessionLastAgentBySessionID = new Map<string, string | null>()
 
 mock.module("../../shared/opencode-storage-detection", () => ({
   isSqliteBackend: () => false,
@@ -20,9 +21,21 @@ mock.module("../../shared/opencode-message-dir", () => ({
   },
 }))
 
+mock.module("../../hooks/atlas/session-last-agent", () => ({
+  getLastAgentFromSession: async (sessionID: string) => {
+    return sessionLastAgentBySessionID.get(sessionID) ?? null
+  },
+}))
+mock.module("../../hooks/atlas/session-last-agent.ts", () => ({
+  getLastAgentFromSession: async (sessionID: string) => {
+    return sessionLastAgentBySessionID.get(sessionID) ?? null
+  },
+}))
+
 afterAll(() => { mock.restore() })
 
 afterEach(() => {
+  sessionLastAgentBySessionID.clear()
   while (testDirs.length > 0) {
     const dir = testDirs.pop()
     if (dir) {
@@ -73,6 +86,7 @@ describe("getContinuationState JSON backend descendant coverage", () => {
     }), "utf-8")
     writeJsonMessage("ses_child_session", "msg_001.json", "atlas")
     writeJsonMessage("ses_child_session", "msg_002.json", "compaction")
+    sessionLastAgentBySessionID.set("ses_child_session", "atlas")
 
     const { getContinuationState } = await import("./continuation-state")
 
@@ -150,6 +164,7 @@ describe("getContinuationState JSON backend descendant coverage", () => {
       model: { providerID: "openai", modelID: "gpt-5.4" },
       time: { created: 100 },
     }), "utf-8")
+    sessionLastAgentBySessionID.set(sessionID, "sisyphus-junior")
 
     const { getContinuationState } = await import("./continuation-state")