ci: restore mock.module() overrides in afterAll to prevent cross-file pollution

Add afterAll hooks that restore original module implementations after
mock.module() overrides. This prevents mock state from leaking across
test files when bun runs them in the same process. Pattern: capture
original module with await import() before mocking, restore in afterAll.

src/cli/doctor/formatter.test.ts

@@ -1,6 +1,10 @@
-import { afterEach, describe, expect, it, mock } from "bun:test"
+import { afterEach, afterAll, describe, expect, it, mock } from "bun:test"
 import type { DoctorResult } from "./types"
 
+const realFormatDefault = await import("./format-default")
+const realFormatStatus = await import("./format-status")
+const realFormatVerbose = await import("./format-verbose")
+
 function createDoctorResult(): DoctorResult {
   return {
     results: [
@@ -44,6 +48,12 @@ describe("formatter", () => {
     mock.restore()
   })
 
+  afterAll(() => {
+    mock.module("./format-default", () => ({ ...realFormatDefault }))
+    mock.module("./format-status", () => ({ ...realFormatStatus }))
+    mock.module("./format-verbose", () => ({ ...realFormatVerbose }))
+  })
+
   describe("formatDoctorOutput", () => {
     it("dispatches to default formatter for default mode", async () => {
       //#given

src/cli/doctor/runner.test.ts

@@ -1,6 +1,9 @@
-import { afterEach, describe, expect, it, mock } from "bun:test"
+import { afterEach, afterAll, describe, expect, it, mock } from "bun:test"
 import type { CheckDefinition, CheckResult, DoctorResult, SystemInfo, ToolsSummary } from "./types"
 
+const realChecks = await import("./checks")
+const realFormatter = await import("./formatter")
+
 function createSystemInfo(): SystemInfo {
   return {
     opencodeVersion: "1.0.200",
@@ -47,6 +50,11 @@ describe("runner", () => {
     mock.restore()
   })
 
+  afterAll(() => {
+    mock.module("./checks", () => ({ ...realChecks }))
+    mock.module("./formatter", () => ({ ...realFormatter }))
+  })
+
   describe("runCheck", () => {
     it("returns fail result with issue when check throws", async () => {
       //#given

src/cli/mcp-oauth/login.test.ts

@@ -1,4 +1,6 @@
-import { describe, it, expect, beforeEach, afterEach, mock } from "bun:test"
+import { describe, it, expect, beforeEach, afterEach, afterAll, mock } from "bun:test"
+
+const realMcpOauthProvider = await import("../../features/mcp-oauth/provider")
 
 const mockLogin = mock(() => Promise.resolve({ accessToken: "test-token", expiresAt: 1710000000 }))
 
@@ -11,6 +13,10 @@ mock.module("../../features/mcp-oauth/provider", () => ({
   },
 }))
 
+afterAll(() => {
+  mock.module("../../features/mcp-oauth/provider", () => ({ ...realMcpOauthProvider }))
+})
+
 const { login } = await import("./login")
 
 describe("login command", () => {

src/cli/run/integration.test.ts

@@ -1,10 +1,13 @@
-import { describe, it, expect, mock, spyOn, beforeEach, afterEach } from "bun:test"
+import { describe, it, expect, mock, spyOn, beforeEach, afterEach, afterAll } from "bun:test"
 import type { RunResult } from "./types"
 import { createJsonOutputManager } from "./json-output"
 import { resolveSession } from "./session-resolver"
 import { executeOnCompleteHook } from "./on-complete-hook"
 import type { OpencodeClient } from "./types"
 
+const realSdk = await import("@opencode-ai/sdk")
+const realPortUtils = await import("../../shared/port-utils")
+
 const mockServerClose = mock(() => {})
 const mockCreateOpencode = mock(() =>
   Promise.resolve({
@@ -17,16 +20,23 @@ const mockIsPortAvailable = mock(() => Promise.resolve(true))
 const mockGetAvailableServerPort = mock(() => Promise.resolve({ port: 9999, wasAutoSelected: false }))
 
 mock.module("@opencode-ai/sdk", () => ({
+  ...realSdk,
   createOpencode: mockCreateOpencode,
   createOpencodeClient: mockCreateOpencodeClient,
 }))
 
 mock.module("../../shared/port-utils", () => ({
+  ...realPortUtils,
   isPortAvailable: mockIsPortAvailable,
   getAvailableServerPort: mockGetAvailableServerPort,
   DEFAULT_SERVER_PORT: 4096,
 }))
 
+afterAll(() => {
+  mock.module("@opencode-ai/sdk", () => ({ ...realSdk }))
+  mock.module("../../shared/port-utils", () => ({ ...realPortUtils }))
+})
+
 const { createServerConnection } = await import("./server-connection")
 
 interface MockWriteStream {

src/cli/run/server-connection.test.ts

@@ -1,4 +1,7 @@
-import { describe, it, expect, mock, beforeEach, afterEach } from "bun:test"
+import { describe, it, expect, mock, beforeEach, afterEach, afterAll } from "bun:test"
+
+const realSdk = await import("@opencode-ai/sdk")
+const realPortUtils = await import("../../shared/port-utils")
 
 const originalConsole = globalThis.console
 
@@ -15,16 +18,23 @@ const mockGetAvailableServerPort = mock(() => Promise.resolve({ port: 4096, wasA
 const mockConsoleLog = mock(() => {})
 
 mock.module("@opencode-ai/sdk", () => ({
+  ...realSdk,
   createOpencode: mockCreateOpencode,
   createOpencodeClient: mockCreateOpencodeClient,
 }))
 
 mock.module("../../shared/port-utils", () => ({
+  ...realPortUtils,
   isPortAvailable: mockIsPortAvailable,
   getAvailableServerPort: mockGetAvailableServerPort,
   DEFAULT_SERVER_PORT: 4096,
 }))
 
+afterAll(() => {
+  mock.module("@opencode-ai/sdk", () => ({ ...realSdk }))
+  mock.module("../../shared/port-utils", () => ({ ...realPortUtils }))
+})
+
 const { createServerConnection } = await import("./server-connection")
 
 describe("createServerConnection", () => {

src/features/claude-code-mcp-loader/loader.test.ts

@@ -6,15 +6,20 @@ import { tmpdir } from "os"
 const TEST_DIR = join(tmpdir(), "mcp-loader-test-" + Date.now())
 const TEST_HOME = join(TEST_DIR, "home")
 
+const realOs = await import("os")
+const realShared = await import("../../shared")
+
 describe("getSystemMcpServerNames", () => {
   beforeEach(() => {
     mkdirSync(TEST_DIR, { recursive: true })
     mkdirSync(TEST_HOME, { recursive: true })
     mock.module("os", () => ({
+      ...realOs,
       homedir: () => TEST_HOME,
       tmpdir,
     }))
     mock.module("../../shared", () => ({
+      ...realShared,
       getClaudeConfigDir: () => join(TEST_HOME, ".claude"),
     }))
   })
@@ -22,6 +27,9 @@ describe("getSystemMcpServerNames", () => {
   afterEach(() => {
     mock.restore()
     rmSync(TEST_DIR, { recursive: true, force: true })
+
+    mock.module("os", () => ({ ...realOs }))
+    mock.module("../../shared", () => ({ ...realShared }))
   })
 
   it("returns empty set when no .mcp.json files exist", async () => {

src/features/skill-mcp-manager/manager.test.ts

@@ -1,8 +1,13 @@
-import { describe, it, expect, beforeEach, afterEach, mock, spyOn } from "bun:test"
+import { describe, it, expect, beforeEach, afterEach, mock, spyOn, afterAll } from "bun:test"
 import { SkillMcpManager } from "./manager"
 import type { SkillMcpClientInfo, SkillMcpServerContext } from "./types"
 import type { ClaudeCodeMcpServer } from "../claude-code-mcp-loader/types"
 
+const realStreamableHttp = await import(
+  "@modelcontextprotocol/sdk/client/streamableHttp.js"
+)
+const realMcpOauthProvider = await import("../mcp-oauth/provider")
+
 // Mock the MCP SDK transports to avoid network calls
 const mockHttpConnect = mock(() => Promise.reject(new Error("Mocked HTTP connection failure")))
 const mockHttpClose = mock(() => Promise.resolve())
@@ -37,6 +42,13 @@ mock.module("../mcp-oauth/provider", () => ({
   },
 }))
 
+afterAll(() => {
+  mock.module("@modelcontextprotocol/sdk/client/streamableHttp.js", () => ({
+    ...realStreamableHttp,
+  }))
+  mock.module("../mcp-oauth/provider", () => ({ ...realMcpOauthProvider }))
+})
+
 
 
 

src/features/tmux-subagent/manager.test.ts

@@ -1,9 +1,13 @@
-import { describe, test, expect, mock, beforeEach } from 'bun:test'
+import { describe, test, expect, mock, beforeEach, afterAll } from 'bun:test'
 import type { TmuxConfig } from '../../config/schema'
 import type { WindowState, PaneAction } from './types'
 import type { ActionResult, ExecuteContext } from './action-executor'
 import type { TmuxUtilDeps } from './manager'
 
+const realPaneStateQuerier = await import('./pane-state-querier')
+const realActionExecutor = await import('./action-executor')
+const realSharedTmux = await import('../../shared/tmux')
+
 type ExecuteActionsResult = {
   success: boolean
   spawnedPaneId?: string
@@ -71,6 +75,12 @@ mock.module('../../shared/tmux', () => {
   }
 })
 
+afterAll(() => {
+  mock.module('./pane-state-querier', () => ({ ...realPaneStateQuerier }))
+  mock.module('./action-executor', () => ({ ...realActionExecutor }))
+  mock.module('../../shared/tmux', () => ({ ...realSharedTmux }))
+})
+
 const trackedSessions = new Set<string>()
 
 function createMockContext(overrides?: {

src/hooks/anthropic-context-window-limit-recovery/storage.test.ts

@@ -1,4 +1,4 @@
-import { describe, test, expect, mock, beforeEach } from "bun:test"
+import { describe, test, expect, mock, beforeEach, afterAll } from "bun:test"
 import { truncateUntilTargetTokens } from "./storage"
 import * as storage from "./storage"
 
@@ -11,6 +11,10 @@ mock.module("./storage", () => {
   }
 })
 
+afterAll(() => {
+  mock.module("./storage", () => ({ ...storage }))
+})
+
 describe("truncateUntilTargetTokens", () => {
   const sessionID = "test-session"
   

src/hooks/auto-update-checker/hook/background-update-check.test.ts

@@ -1,4 +1,11 @@
-import { describe, it, expect, mock, beforeEach } from "bun:test"
+import { describe, it, expect, mock, beforeEach, afterAll } from "bun:test"
+
+const realChecker = await import("../checker")
+const realVersionChannel = await import("../version-channel")
+const realCache = await import("../cache")
+const realConfigManager = await import("../../../cli/config-manager")
+const realUpdateToasts = await import("./update-toasts")
+const realLogger = await import("../../../shared/logger")
 
 // Mock modules before importing
 const mockFindPluginEntry = mock(() => null as any)
@@ -39,6 +46,15 @@ mock.module("../../../shared/logger", () => ({
   log: () => {},
 }))
 
+afterAll(() => {
+  mock.module("../checker", () => ({ ...realChecker }))
+  mock.module("../version-channel", () => ({ ...realVersionChannel }))
+  mock.module("../cache", () => ({ ...realCache }))
+  mock.module("../../../cli/config-manager", () => ({ ...realConfigManager }))
+  mock.module("./update-toasts", () => ({ ...realUpdateToasts }))
+  mock.module("../../../shared/logger", () => ({ ...realLogger }))
+})
+
 const { runBackgroundUpdateCheck } = await import("./background-update-check")
 
 describe("runBackgroundUpdateCheck", () => {

src/hooks/claude-code-hooks/stop.test.ts

@@ -1,7 +1,10 @@
-import { describe, it, expect, mock, beforeEach } from "bun:test"
+import { describe, it, expect, mock, beforeEach, afterAll } from "bun:test"
 import type { ClaudeHooksConfig } from "./types"
 import type { StopContext } from "./stop"
 
+const realCommandExecutor = await import("../../shared/command-executor")
+const realLogger = await import("../../shared/logger")
+
 const mockExecuteHookCommand = mock(() =>
   Promise.resolve({ exitCode: 0, stdout: "", stderr: "" })
 )
@@ -17,6 +20,11 @@ mock.module("../../shared/logger", () => ({
   getLogFilePath: () => "/tmp/test.log",
 }))
 
+afterAll(() => {
+  mock.module("../../shared/command-executor", () => ({ ...realCommandExecutor }))
+  mock.module("../../shared/logger", () => ({ ...realLogger }))
+})
+
 const { executeStopHooks } = await import("./stop")
 
 function createStopContext(overrides?: Partial<StopContext>): StopContext {

src/hooks/comment-checker/cli.test.ts

@@ -1,10 +1,19 @@
-import { describe, test, expect, mock } from "bun:test"
+import { describe, test, expect, mock, afterAll } from "bun:test"
 import { chmodSync, mkdtempSync, writeFileSync } from "node:fs"
 import { join } from "node:path"
 import { tmpdir } from "node:os"
 
 import type { PendingCall } from "./types"
 
+const realCli = await import("./cli")
+const cliTsHref = new URL("./cli.ts", import.meta.url).href
+
+afterAll(() => {
+  mock.module("./cli", () => ({ ...realCli }))
+  mock.module("./cli.ts", () => ({ ...realCli }))
+  mock.module(cliTsHref, () => ({ ...realCli }))
+})
+
 function createMockInput() {
   return {
     session_id: "test",

src/hooks/comment-checker/hook.apply-patch.test.ts

@@ -1,4 +1,6 @@
-import { describe, it, expect, mock, beforeEach } from "bun:test"
+import { describe, it, expect, mock, beforeEach, afterAll } from "bun:test"
+
+const realCliRunner = await import("./cli-runner")
 
 const processApplyPatchEditsWithCli = mock(async () => {})
 
@@ -10,6 +12,10 @@ mock.module("./cli-runner", () => ({
   processApplyPatchEditsWithCli,
 }))
 
+afterAll(() => {
+  mock.module("./cli-runner", () => ({ ...realCliRunner }))
+})
+
 const { createCommentCheckerHooks } = await import("./hook")
 
 describe("comment-checker apply_patch integration", () => {

src/hooks/compaction-context-injector/index.test.ts

@@ -1,4 +1,6 @@
-import { describe, expect, it, mock } from "bun:test"
+import { describe, expect, it, mock, afterAll } from "bun:test"
+
+const realSystemDirective = await import("../../shared/system-directive")
 
 mock.module("../../shared/system-directive", () => ({
   createSystemDirective: (type: string) => `[DIRECTIVE:${type}]`,
@@ -14,6 +16,10 @@ mock.module("../../shared/system-directive", () => ({
   },
 }))
 
+afterAll(() => {
+  mock.module("../../shared/system-directive", () => ({ ...realSystemDirective }))
+})
+
 import { createCompactionContextInjector } from "./index"
 import { TaskHistory } from "../../features/background-agent/task-history"
 

src/hooks/rules-injector/injector.test.ts

@@ -1,4 +1,4 @@
-import { afterEach, beforeEach, describe, expect, it, mock } from "bun:test";
+import { afterEach, beforeEach, describe, expect, it, mock, afterAll } from "bun:test";
 import * as fs from "node:fs";
 import { mkdirSync, rmSync, writeFileSync } from "node:fs";
 import * as os from "node:os";
@@ -6,6 +6,10 @@ import { tmpdir } from "node:os";
 import { join } from "node:path";
 import { RULES_INJECTOR_STORAGE } from "./constants";
 
+const realNodeFs = await import("node:fs");
+const realNodeOs = await import("node:os");
+const realMatcher = await import("./matcher");
+
 type StatSnapshot = { mtimeMs: number; size: number };
 
 let trackedRulePath = "";
@@ -56,6 +60,12 @@ mock.module("./matcher", () => ({
   isDuplicateByContentHash: (hash: string, cache: Set<string>) => cache.has(hash),
 }));
 
+afterAll(() => {
+  mock.module("node:fs", () => ({ ...realNodeFs }));
+  mock.module("node:os", () => ({ ...realNodeOs }));
+  mock.module("./matcher", () => ({ ...realMatcher }));
+});
+
 function createOutput(): { title: string; output: string; metadata: unknown } {
   return { title: "tool", output: "", metadata: {} };
 }

src/tools/lsp/client.test.ts

@@ -2,7 +2,9 @@ import { mkdtempSync, rmSync, writeFileSync } from "node:fs"
 import { join } from "node:path"
 import { tmpdir } from "node:os"
 
-import { describe, it, expect, spyOn, mock, beforeEach, afterEach } from "bun:test"
+import { describe, it, expect, spyOn, mock, beforeEach, afterEach, afterAll } from "bun:test"
+
+const realJsonRpcNode = await import("vscode-jsonrpc/node")
 
 mock.module("vscode-jsonrpc/node", () => ({
   createMessageConnection: () => {
@@ -12,6 +14,10 @@ mock.module("vscode-jsonrpc/node", () => ({
   StreamMessageWriter: function StreamMessageWriter() {},
 }))
 
+afterAll(() => {
+  mock.module("vscode-jsonrpc/node", () => ({ ...realJsonRpcNode }))
+})
+
 import { LSPClient, lspManager, validateCwd } from "./client"
 import type { ResolvedServer } from "./types"
 

src/tools/session-manager/storage.test.ts

@@ -1,9 +1,11 @@
-import { describe, test, expect, beforeEach, afterEach, mock } from "bun:test"
+import { describe, test, expect, beforeEach, afterEach, afterAll, mock } from "bun:test"
 import { mkdirSync, writeFileSync, rmSync, existsSync } from "node:fs"
 import { join } from "node:path"
 import { tmpdir } from "node:os"
 import { randomUUID } from "node:crypto"
 
+const realConstants = await import("./constants")
+
 const TEST_DIR = join(tmpdir(), `omo-test-session-manager-${randomUUID()}`)
 const TEST_MESSAGE_STORAGE = join(TEST_DIR, "message")
 const TEST_PART_STORAGE = join(TEST_DIR, "part")
@@ -26,6 +28,10 @@ mock.module("./constants", () => ({
   TOOL_NAME_PREFIX: "session_",
 }))
 
+afterAll(() => {
+  mock.module("./constants", () => ({ ...realConstants }))
+})
+
 const { getAllSessions, getMessageDir, sessionExists, readSessionMessages, readSessionTodos, getSessionInfo } =
   await import("./storage")
 

src/tools/skill/tools.test.ts

@@ -1,4 +1,4 @@
-import { describe, it, expect, beforeEach, mock, spyOn } from "bun:test"
+import { describe, it, expect, beforeEach, mock, spyOn, afterAll } from "bun:test"
 import type { ToolContext } from "@opencode-ai/plugin/tool"
 import * as fs from "node:fs"
 import { createSkillTool } from "./tools"
@@ -8,6 +8,8 @@ import type { Tool as McpTool } from "@modelcontextprotocol/sdk/types.js"
 
 const originalReadFileSync = fs.readFileSync.bind(fs)
 
+const realNodeFs = await import("node:fs")
+
 mock.module("node:fs", () => ({
   ...fs,
   readFileSync: (path: string, encoding?: string) => {
@@ -21,6 +23,10 @@ Test skill body content`
   },
 }))
 
+afterAll(() => {
+  mock.module("node:fs", () => ({ ...realNodeFs }))
+})
+
 function createMockSkill(name: string, options: { agent?: string } = {}): LoadedSkill {
   return {
     name,