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.

.github/workflows/ci.yml

@@ -52,12 +52,31 @@ jobs:
           bun test src/hooks/atlas
           bun test src/hooks/compaction-context-injector
           bun test src/features/tmux-subagent
+          bun test src/cli/doctor/formatter.test.ts
+          bun test src/cli/doctor/format-default.test.ts
+          bun test src/tools/call-omo-agent/sync-executor.test.ts
+          bun test src/tools/call-omo-agent/session-creator.test.ts
+          bun test src/features/opencode-skill-loader/loader.test.ts
 
       - name: Run remaining tests
         run: |
-          # Run all other tests (mock-heavy ones are re-run but that's acceptable)
-          bun test bin script src/cli src/config src/mcp src/index.test.ts \
-            src/agents src/tools src/shared \
+          # Enumerate subdirectories/files explicitly to EXCLUDE mock-heavy files
+          # that were already run in isolation above.
+          # Excluded from src/cli: doctor/formatter.test.ts, doctor/format-default.test.ts
+          # Excluded from src/tools: call-omo-agent/sync-executor.test.ts, call-omo-agent/session-creator.test.ts
+          bun test bin script src/config src/mcp src/index.test.ts \
+            src/agents src/shared \
+            src/cli/run src/cli/config-manager src/cli/mcp-oauth \
+            src/cli/index.test.ts src/cli/install.test.ts src/cli/model-fallback.test.ts \
+            src/cli/config-manager.test.ts \
+            src/cli/doctor/runner.test.ts src/cli/doctor/checks \
+            src/tools/ast-grep src/tools/background-task src/tools/delegate-task \
+            src/tools/glob src/tools/grep src/tools/interactive-bash \
+            src/tools/look-at src/tools/lsp src/tools/session-manager \
+            src/tools/skill src/tools/skill-mcp src/tools/slashcommand src/tools/task \
+            src/tools/call-omo-agent/background-agent-executor.test.ts \
+            src/tools/call-omo-agent/background-executor.test.ts \
+            src/tools/call-omo-agent/subagent-session-creator.test.ts \
             src/hooks/anthropic-context-window-limit-recovery \
             src/hooks/claude-code-compatibility \
             src/hooks/context-injection \
@@ -70,7 +89,11 @@ jobs:
             src/features/builtin-skills \
             src/features/claude-code-session-state \
             src/features/hook-message-injector \
-            src/features/opencode-skill-loader \
+            src/features/opencode-skill-loader/config-source-discovery.test.ts \
+            src/features/opencode-skill-loader/merger.test.ts \
+            src/features/opencode-skill-loader/skill-content.test.ts \
+            src/features/opencode-skill-loader/blocking.test.ts \
+            src/features/opencode-skill-loader/async-loader.test.ts \
             src/features/skill-mcp-manager
 
   typecheck:

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/background-agent/manager.ts

@@ -7,6 +7,7 @@ import type {
 } from "./types"
 import { TaskHistory } from "./task-history"
 import { log, getAgentToolRestrictions, promptWithModelSuggestionRetry } from "../../shared"
+import { setSessionTools } from "../../shared/session-tools-store"
 import { ConcurrencyManager } from "./concurrency"
 import type { BackgroundTaskConfig, TmuxConfig } from "../../config/schema"
 import { isInsideTmux } from "../../shared/tmux"
@@ -141,6 +142,7 @@ export class BackgroundManager {
       parentMessageID: input.parentMessageID,
       parentModel: input.parentModel,
       parentAgent: input.parentAgent,
+      parentTools: input.parentTools,
       model: input.model,
       category: input.category,
     }
@@ -328,12 +330,16 @@ export class BackgroundManager {
         ...(launchModel ? { model: launchModel } : {}),
         ...(launchVariant ? { variant: launchVariant } : {}),
         system: input.skillContent,
-        tools: {
-          ...getAgentToolRestrictions(input.agent),
-          task: false,
-          call_omo_agent: true,
-          question: false,
-        },
+        tools: (() => {
+          const tools = {
+            ...getAgentToolRestrictions(input.agent),
+            task: false,
+            call_omo_agent: true,
+            question: false,
+          }
+          setSessionTools(sessionID, tools)
+          return tools
+        })(),
         parts: [{ type: "text", text: input.prompt }],
       },
     }).catch((error) => {
@@ -535,6 +541,9 @@ export class BackgroundManager {
     existingTask.parentMessageID = input.parentMessageID
     existingTask.parentModel = input.parentModel
     existingTask.parentAgent = input.parentAgent
+    if (input.parentTools) {
+      existingTask.parentTools = input.parentTools
+    }
     // Reset startedAt on resume to prevent immediate completion
     // The MIN_IDLE_TIME_MS check uses startedAt, so resumed tasks need fresh timing
     existingTask.startedAt = new Date()
@@ -588,12 +597,16 @@ export class BackgroundManager {
         agent: existingTask.agent,
         ...(resumeModel ? { model: resumeModel } : {}),
         ...(resumeVariant ? { variant: resumeVariant } : {}),
-        tools: {
-          ...getAgentToolRestrictions(existingTask.agent),
-          task: false,
-          call_omo_agent: true,
-          question: false,
-        },
+        tools: (() => {
+          const tools = {
+            ...getAgentToolRestrictions(existingTask.agent),
+            task: false,
+            call_omo_agent: true,
+            question: false,
+          }
+          setSessionTools(existingTask.sessionID!, tools)
+          return tools
+        })(),
         parts: [{ type: "text", text: input.prompt }],
       },
     }).catch((error) => {
@@ -1252,6 +1265,7 @@ Use \`background_output(task_id="${task.id}")\` to retrieve this result when rea
           noReply: !allComplete,
           ...(agent !== undefined ? { agent } : {}),
           ...(model !== undefined ? { model } : {}),
+          ...(task.parentTools ? { tools: task.parentTools } : {}),
           parts: [{ type: "text", text: notification }],
         },
       })

src/features/background-agent/notify-parent-session.ts

@@ -148,6 +148,7 @@ export async function notifyParentSession(args: {
         noReply: !allComplete,
         ...(agent !== undefined ? { agent } : {}),
         ...(model !== undefined ? { model } : {}),
+        ...(task.parentTools ? { tools: task.parentTools } : {}),
         parts: [{ type: "text", text: notification }],
       },
     })

src/features/background-agent/parent-session-notifier.ts

@@ -71,6 +71,7 @@ export async function notifyParentSession(
         noReply: !allComplete,
         ...(agent !== undefined ? { agent } : {}),
         ...(model !== undefined ? { model } : {}),
+        ...(task.parentTools ? { tools: task.parentTools } : {}),
         parts: [{ type: "text", text: notification }],
       },
     })

src/features/background-agent/spawner/task-factory.ts

@@ -13,6 +13,7 @@ export function createTask(input: LaunchInput): BackgroundTask {
     parentMessageID: input.parentMessageID,
     parentModel: input.parentModel,
     parentAgent: input.parentAgent,
+    parentTools: input.parentTools,
     model: input.model,
   }
 }

src/features/background-agent/spawner/task-resumer.ts

@@ -1,5 +1,6 @@
 import type { BackgroundTask, ResumeInput } from "../types"
 import { log, getAgentToolRestrictions } from "../../../shared"
+import { setSessionTools } from "../../../shared/session-tools-store"
 import type { SpawnerContext } from "./spawner-context"
 import { subagentSessions } from "../../claude-code-session-state"
 import { getTaskToastManager } from "../../task-toast-manager"
@@ -35,6 +36,9 @@ export async function resumeTask(
   task.parentMessageID = input.parentMessageID
   task.parentModel = input.parentModel
   task.parentAgent = input.parentAgent
+  if (input.parentTools) {
+    task.parentTools = input.parentTools
+  }
   task.startedAt = new Date()
 
   task.progress = {
@@ -75,12 +79,16 @@ export async function resumeTask(
         agent: task.agent,
         ...(resumeModel ? { model: resumeModel } : {}),
         ...(resumeVariant ? { variant: resumeVariant } : {}),
-        tools: {
-          ...getAgentToolRestrictions(task.agent),
-          task: false,
-          call_omo_agent: true,
-          question: false,
-        },
+        tools: (() => {
+          const tools = {
+            ...getAgentToolRestrictions(task.agent),
+            task: false,
+            call_omo_agent: true,
+            question: false,
+          }
+          setSessionTools(task.sessionID!, tools)
+          return tools
+        })(),
         parts: [{ type: "text", text: input.prompt }],
       },
     })

src/features/background-agent/spawner/task-starter.ts

@@ -1,5 +1,6 @@
 import type { QueueItem } from "../constants"
 import { log, getAgentToolRestrictions, promptWithModelSuggestionRetry } from "../../../shared"
+import { setSessionTools } from "../../../shared/session-tools-store"
 import { subagentSessions } from "../../claude-code-session-state"
 import { getTaskToastManager } from "../../task-toast-manager"
 import { createBackgroundSession } from "./background-session-creator"
@@ -79,12 +80,16 @@ export async function startTask(item: QueueItem, ctx: SpawnerContext): Promise<v
       ...(launchModel ? { model: launchModel } : {}),
       ...(launchVariant ? { variant: launchVariant } : {}),
       system: input.skillContent,
-      tools: {
-        ...getAgentToolRestrictions(input.agent),
-        task: false,
-        call_omo_agent: true,
-        question: false,
-      },
+      tools: (() => {
+        const tools = {
+          ...getAgentToolRestrictions(input.agent),
+          task: false,
+          call_omo_agent: true,
+          question: false,
+        }
+        setSessionTools(sessionID, tools)
+        return tools
+      })(),
       parts: [{ type: "text", text: input.prompt }],
     },
   }).catch((error: unknown) => {

src/features/background-agent/types.ts

@@ -37,6 +37,8 @@ export interface BackgroundTask {
   concurrencyGroup?: string
   /** Parent session's agent name for notification */
   parentAgent?: string
+  /** Parent session's tool restrictions for notification prompts */
+  parentTools?: Record<string, boolean>
   /** Marks if the task was launched from an unstable agent/category */
   isUnstableAgent?: boolean
   /** Category used for this task (e.g., 'quick', 'visual-engineering') */
@@ -56,6 +58,7 @@ export interface LaunchInput {
   parentMessageID: string
   parentModel?: { providerID: string; modelID: string }
   parentAgent?: string
+  parentTools?: Record<string, boolean>
   model?: { providerID: string; modelID: string; variant?: string }
   isUnstableAgent?: boolean
   skills?: string[]
@@ -70,4 +73,5 @@ export interface ResumeInput {
   parentMessageID: string
   parentModel?: { providerID: string; modelID: string }
   parentAgent?: string
+  parentTools?: Record<string, boolean>
 }

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/opencode-skill-loader/config-source-discovery.ts

@@ -53,26 +53,28 @@ async function loadSourcePath(options: {
   const stat = await fs.stat(absolutePath).catch(() => null)
   if (!stat) return []
 
+  const realBasePath = await fs.realpath(absolutePath).catch(() => absolutePath)
+
   if (stat.isFile()) {
-    if (!isMarkdownPath(absolutePath)) return []
+    if (!isMarkdownPath(realBasePath)) return []
     const loaded = await loadSkillFromPath({
-      skillPath: absolutePath,
-      resolvedPath: dirname(absolutePath),
-      defaultName: inferSkillNameFromFileName(absolutePath),
+      skillPath: realBasePath,
+      resolvedPath: dirname(realBasePath),
+      defaultName: inferSkillNameFromFileName(realBasePath),
       scope: "config",
     })
     if (!loaded) return []
-    return filterByGlob([loaded], dirname(absolutePath), options.globPattern)
+    return filterByGlob([loaded], dirname(realBasePath), options.globPattern)
   }
 
   if (!stat.isDirectory()) return []
 
   const directorySkills = await loadSkillsFromDir({
-    skillsDir: absolutePath,
+    skillsDir: realBasePath,
     scope: "config",
     maxDepth: options.recursive ? MAX_RECURSIVE_DEPTH : 0,
   })
-  return filterByGlob(directorySkills, absolutePath, options.globPattern)
+  return filterByGlob(directorySkills, realBasePath, options.globPattern)
 }
 
 export async function discoverConfigSourceSkills(options: {

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/recovery-deduplication.test.ts

@@ -1,13 +1,21 @@
-import { describe, test, expect, mock, beforeEach } from "bun:test"
+import { describe, test, expect, mock, beforeEach, afterAll } from "bun:test"
 import type { PluginInput } from "@opencode-ai/plugin"
 import type { ExperimentalConfig } from "../../config"
 
-const attemptDeduplicationRecoveryMock = mock(async () => {})
+const realDeduplicationRecovery = await import("./deduplication-recovery")
+
+const attemptDeduplicationRecoveryMock = mock<(sessionID: string) => Promise<void>>(
+  async () => {}
+)
 
 mock.module("./deduplication-recovery", () => ({
   attemptDeduplicationRecovery: attemptDeduplicationRecoveryMock,
 }))
 
+afterAll(() => {
+  mock.module("./deduplication-recovery", () => ({ ...realDeduplicationRecovery }))
+})
+
 function createImmediateTimeouts(): () => void {
   const originalSetTimeout = globalThis.setTimeout
   const originalClearTimeout = globalThis.clearTimeout
@@ -37,13 +45,15 @@ describe("createAnthropicContextWindowLimitRecoveryHook", () => {
     const experimental = {
       dynamic_context_pruning: {
         enabled: true,
+        notification: "off",
+        protected_tools: [],
         strategies: {
           deduplication: { enabled: true },
         },
       },
     } satisfies ExperimentalConfig
 
-    let resolveSummarize: (() => void) | null = null
+    let resolveSummarize: ((value?: void) => void) | null = null
     const summarizePromise = new Promise<void>((resolve) => {
       resolveSummarize = resolve
     })
@@ -62,7 +72,7 @@ describe("createAnthropicContextWindowLimitRecoveryHook", () => {
 
     try {
       const { createAnthropicContextWindowLimitRecoveryHook } = await import("./recovery-hook")
-      const ctx = { client: mockClient, directory: "/tmp" } as PluginInput
+      const ctx = { client: mockClient, directory: "/tmp" } as unknown as PluginInput
       const hook = createAnthropicContextWindowLimitRecoveryHook(ctx, { experimental })
 
       // first error triggers compaction (setTimeout runs immediately due to mock)
@@ -105,7 +115,7 @@ describe("createAnthropicContextWindowLimitRecoveryHook", () => {
     }
 
     const { createAnthropicContextWindowLimitRecoveryHook } = await import("./recovery-hook")
-    const ctx = { client: mockClient, directory: "/tmp" } as PluginInput
+    const ctx = { client: mockClient, directory: "/tmp" } as unknown as PluginInput
     const hook = createAnthropicContextWindowLimitRecoveryHook(ctx)
 
     //#when - single error (no compaction in progress)

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/atlas/index.test.ts

@@ -1,4 +1,4 @@
-import { describe, expect, test, beforeEach, afterEach, mock } from "bun:test"
+import { describe, expect, test, beforeEach, afterEach, afterAll, mock } from "bun:test"
 import { existsSync, mkdirSync, rmSync, writeFileSync } from "node:fs"
 import { join } from "node:path"
 import { tmpdir } from "node:os"
@@ -9,20 +9,19 @@ import {
   readBoulderState,
 } from "../../features/boulder-state"
 import type { BoulderState } from "../../features/boulder-state"
-
-const TEST_STORAGE_ROOT = join(tmpdir(), `atlas-message-storage-${randomUUID()}`)
-const TEST_MESSAGE_STORAGE = join(TEST_STORAGE_ROOT, "message")
-const TEST_PART_STORAGE = join(TEST_STORAGE_ROOT, "part")
-
-mock.module("../../features/hook-message-injector/constants", () => ({
-  OPENCODE_STORAGE: TEST_STORAGE_ROOT,
-  MESSAGE_STORAGE: TEST_MESSAGE_STORAGE,
-  PART_STORAGE: TEST_PART_STORAGE,
-}))
+const realClaudeCodeSessionState = await import(
+  "../../features/claude-code-session-state"
+)
 
 const { createAtlasHook } = await import("./index")
 const { MESSAGE_STORAGE } = await import("../../features/hook-message-injector")
 
+afterAll(() => {
+  mock.module("../../features/claude-code-session-state", () => ({
+    ...realClaudeCodeSessionState,
+  }))
+})
+
 describe("atlas hook", () => {
   let TEST_DIR: string
   let SISYPHUS_DIR: string
@@ -77,7 +76,6 @@ describe("atlas hook", () => {
     if (existsSync(TEST_DIR)) {
       rmSync(TEST_DIR, { recursive: true, force: true })
     }
-    rmSync(TEST_STORAGE_ROOT, { recursive: true, force: true })
   })
 
   describe("tool.execute.after handler", () => {

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/compaction-todo-preserver/index.test.ts

@@ -30,7 +30,7 @@ function createMockContext(todoResponses: TodoSnapshot[][]): PluginInput {
       },
     },
     directory: "/tmp/test",
-  } as PluginInput
+  } as unknown as PluginInput
 }
 
 describe("compaction-todo-preserver", () => {
@@ -38,7 +38,7 @@ describe("compaction-todo-preserver", () => {
     //#given
     updateMock.mockClear()
     const sessionID = "session-compaction-missing"
-    const todos = [
+    const todos: TodoSnapshot[] = [
       { id: "1", content: "Task 1", status: "pending", priority: "high" },
       { id: "2", content: "Task 2", status: "in_progress", priority: "medium" },
     ]
@@ -58,7 +58,7 @@ describe("compaction-todo-preserver", () => {
     //#given
     updateMock.mockClear()
     const sessionID = "session-compaction-present"
-    const todos = [
+    const todos: TodoSnapshot[] = [
       { id: "1", content: "Task 1", status: "pending", priority: "high" },
     ]
     const ctx = createMockContext([todos, todos])

src/hooks/directory-agents-injector/injector.test.ts

@@ -1,34 +1,59 @@
-import { beforeEach, describe, expect, it, mock } from "bun:test"
+import { beforeEach, afterEach, describe, expect, it, mock, afterAll } from "bun:test"
 
-const readFileSyncMock = mock((_: string, __: string) => "# AGENTS")
+const realNodeFs = await import("node:fs")
+const realFinder = await import("./finder")
+const realStorage = await import("./storage")
+
+const originalReadFileSync = realNodeFs.readFileSync
+const readFileSyncMock = mock((filePath: string, encoding?: string) => {
+  if (String(filePath).endsWith("AGENTS.md")) {
+    return "# AGENTS"
+  }
+  return originalReadFileSync(filePath as never, encoding as never)
+})
 const findAgentsMdUpMock = mock((_: { startDir: string; rootDir: string }) => [] as string[])
 const resolveFilePathMock = mock((_: string, path: string) => path)
 const loadInjectedPathsMock = mock((_: string) => new Set<string>())
 const saveInjectedPathsMock = mock((_: string, __: Set<string>) => {})
 
-mock.module("node:fs", () => ({
-  readFileSync: readFileSyncMock,
-}))
+afterAll(() => {
+  mock.module("node:fs", () => ({ ...realNodeFs }))
+  mock.module("./finder", () => ({ ...realFinder }))
+  mock.module("./storage", () => ({ ...realStorage }))
+})
 
-mock.module("./finder", () => ({
-  findAgentsMdUp: findAgentsMdUpMock,
-  resolveFilePath: resolveFilePathMock,
-}))
-
-mock.module("./storage", () => ({
-  loadInjectedPaths: loadInjectedPathsMock,
-  saveInjectedPaths: saveInjectedPathsMock,
-}))
-
-const { processFilePathForAgentsInjection } = await import("./injector")
+let processFilePathForAgentsInjection: typeof import("./injector").processFilePathForAgentsInjection
 
 describe("processFilePathForAgentsInjection", () => {
-  beforeEach(() => {
+  beforeEach(async () => {
     readFileSyncMock.mockClear()
     findAgentsMdUpMock.mockClear()
     resolveFilePathMock.mockClear()
     loadInjectedPathsMock.mockClear()
     saveInjectedPathsMock.mockClear()
+
+    mock.module("node:fs", () => ({
+      ...realNodeFs,
+      readFileSync: readFileSyncMock,
+    }))
+
+    mock.module("./finder", () => ({
+      findAgentsMdUp: findAgentsMdUpMock,
+      resolveFilePath: resolveFilePathMock,
+    }))
+
+    mock.module("./storage", () => ({
+      loadInjectedPaths: loadInjectedPathsMock,
+      saveInjectedPaths: saveInjectedPathsMock,
+    }))
+
+    ;({ processFilePathForAgentsInjection } = await import(`./injector?${Date.now()}`))
+  })
+
+  afterEach(() => {
+    mock.module("node:fs", () => ({ ...realNodeFs }))
+    mock.module("./finder", () => ({ ...realFinder }))
+    mock.module("./storage", () => ({ ...realStorage }))
   })
 
   it("does not save when all discovered paths are already cached", async () => {

src/hooks/directory-readme-injector/injector.test.ts

@@ -1,34 +1,59 @@
-import { beforeEach, describe, expect, it, mock } from "bun:test"
+import { beforeEach, afterEach, describe, expect, it, mock, afterAll } from "bun:test"
 
-const readFileSyncMock = mock((_: string, __: string) => "# README")
+const realNodeFs = await import("node:fs")
+const realFinder = await import("./finder")
+const realStorage = await import("./storage")
+
+const originalReadFileSync = realNodeFs.readFileSync
+const readFileSyncMock = mock((filePath: string, encoding?: string) => {
+  if (String(filePath).endsWith("README.md")) {
+    return "# README"
+  }
+  return originalReadFileSync(filePath as never, encoding as never)
+})
 const findReadmeMdUpMock = mock((_: { startDir: string; rootDir: string }) => [] as string[])
 const resolveFilePathMock = mock((_: string, path: string) => path)
 const loadInjectedPathsMock = mock((_: string) => new Set<string>())
 const saveInjectedPathsMock = mock((_: string, __: Set<string>) => {})
 
-mock.module("node:fs", () => ({
-  readFileSync: readFileSyncMock,
-}))
+afterAll(() => {
+  mock.module("node:fs", () => ({ ...realNodeFs }))
+  mock.module("./finder", () => ({ ...realFinder }))
+  mock.module("./storage", () => ({ ...realStorage }))
+})
 
-mock.module("./finder", () => ({
-  findReadmeMdUp: findReadmeMdUpMock,
-  resolveFilePath: resolveFilePathMock,
-}))
-
-mock.module("./storage", () => ({
-  loadInjectedPaths: loadInjectedPathsMock,
-  saveInjectedPaths: saveInjectedPathsMock,
-}))
-
-const { processFilePathForReadmeInjection } = await import("./injector")
+let processFilePathForReadmeInjection: typeof import("./injector").processFilePathForReadmeInjection
 
 describe("processFilePathForReadmeInjection", () => {
-  beforeEach(() => {
+  beforeEach(async () => {
     readFileSyncMock.mockClear()
     findReadmeMdUpMock.mockClear()
     resolveFilePathMock.mockClear()
     loadInjectedPathsMock.mockClear()
     saveInjectedPathsMock.mockClear()
+
+    mock.module("node:fs", () => ({
+      ...realNodeFs,
+      readFileSync: readFileSyncMock,
+    }))
+
+    mock.module("./finder", () => ({
+      findReadmeMdUp: findReadmeMdUpMock,
+      resolveFilePath: resolveFilePathMock,
+    }))
+
+    mock.module("./storage", () => ({
+      loadInjectedPaths: loadInjectedPathsMock,
+      saveInjectedPaths: saveInjectedPathsMock,
+    }))
+
+    ;({ processFilePathForReadmeInjection } = await import(`./injector?${Date.now()}`))
+  })
+
+  afterEach(() => {
+    mock.module("node:fs", () => ({ ...realNodeFs }))
+    mock.module("./finder", () => ({ ...realFinder }))
+    mock.module("./storage", () => ({ ...realStorage }))
   })
 
   it("does not save when all discovered paths are already cached", async () => {

src/hooks/prometheus-md-only/index.test.ts

@@ -1,4 +1,4 @@
-import { describe, expect, test, beforeEach, afterEach, mock } from "bun:test"
+import { describe, expect, test, beforeEach, afterEach } from "bun:test"
 import { mkdirSync, rmSync, writeFileSync } from "node:fs"
 import { join } from "node:path"
 import { tmpdir } from "node:os"
@@ -6,16 +6,6 @@ import { randomUUID } from "node:crypto"
 import { SYSTEM_DIRECTIVE_PREFIX } from "../../shared/system-directive"
 import { clearSessionAgent } from "../../features/claude-code-session-state"
 
-const TEST_STORAGE_ROOT = join(tmpdir(), `prometheus-md-only-${randomUUID()}`)
-const TEST_MESSAGE_STORAGE = join(TEST_STORAGE_ROOT, "message")
-const TEST_PART_STORAGE = join(TEST_STORAGE_ROOT, "part")
-
-mock.module("../../features/hook-message-injector/constants", () => ({
-  OPENCODE_STORAGE: TEST_STORAGE_ROOT,
-  MESSAGE_STORAGE: TEST_MESSAGE_STORAGE,
-  PART_STORAGE: TEST_PART_STORAGE,
-}))
-
 const { createPrometheusMdOnlyHook } = await import("./index")
 const { MESSAGE_STORAGE } = await import("../../features/hook-message-injector")
 
@@ -52,7 +42,6 @@ describe("prometheus-md-only", () => {
         // ignore
       }
     }
-    rmSync(TEST_STORAGE_ROOT, { recursive: true, force: true })
   })
 
   describe("agent name matching", () => {

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/hooks/todo-continuation-enforcer/todo-continuation-enforcer.test.ts

@@ -518,7 +518,7 @@ describe("todo-continuation-enforcer", () => {
 
     //#then
     expect(promptCalls).toHaveLength(2)
-  })
+  }, 20000)
 
   test("should keep injecting even when todos remain unchanged across cycles", async () => {
     //#given
@@ -553,7 +553,7 @@ describe("todo-continuation-enforcer", () => {
 
     //#then — all 5 injections should fire (no stagnation cap)
     expect(promptCalls).toHaveLength(5)
-  })
+  }, 30000)
 
   test("should skip idle handling while injection is in flight", async () => {
     //#given
@@ -613,7 +613,7 @@ describe("todo-continuation-enforcer", () => {
 
     //#then
     expect(promptCalls).toHaveLength(2)
-  })
+  }, 20000)
 
   test("should accept skipAgents option without error", async () => {
     // given - session with skipAgents configured for Prometheus

src/shared/agents-config-dir.test.ts

@@ -0,0 +1,14 @@
+import { describe, test, expect } from "bun:test"
+import { getAgentsConfigDir } from "./agents-config-dir"
+
+describe("getAgentsConfigDir", () => {
+  test("returns path ending with .agents", () => {
+    // given agents config dir is requested
+
+    // when getAgentsConfigDir is called
+    const result = getAgentsConfigDir()
+
+    // then returns path ending with .agents
+    expect(result.endsWith(".agents")).toBe(true)
+  })
+})

src/shared/agents-config-dir.ts

@@ -0,0 +1,6 @@
+import { homedir } from "node:os"
+import { join } from "node:path"
+
+export function getAgentsConfigDir(): string {
+  return join(homedir(), ".agents")
+}

src/shared/file-utils.test.ts

@@ -0,0 +1,103 @@
+import { describe, it, expect, beforeAll, afterAll } from "bun:test"
+import { mkdirSync, writeFileSync, symlinkSync, rmSync, realpathSync } from "fs"
+import { join } from "path"
+import { tmpdir } from "os"
+import { resolveSymlink, resolveSymlinkAsync, isSymbolicLink } from "./file-utils"
+
+const testDir = join(realpathSync(tmpdir()), "file-utils-test-" + Date.now())
+
+// Create a directory structure that mimics the real-world scenario:
+//
+//   testDir/
+//   ├── repo/
+//   │   ├── skills/
+//   │   │   └── category/
+//   │   │       └── my-skill/
+//   │   │           └── SKILL.md
+//   │   └── .opencode/
+//   │       └── skills/
+//   │           └── my-skill -> ../../skills/category/my-skill  (relative symlink)
+//   └── config/
+//       └── skills -> ../repo/.opencode/skills                  (absolute symlink)
+
+const realSkillDir = join(testDir, "repo", "skills", "category", "my-skill")
+const repoOpencodeSkills = join(testDir, "repo", ".opencode", "skills")
+const configSkills = join(testDir, "config", "skills")
+
+beforeAll(() => {
+	// Create real skill directory with a file
+	mkdirSync(realSkillDir, { recursive: true })
+	writeFileSync(join(realSkillDir, "SKILL.md"), "# My Skill")
+
+	// Create .opencode/skills/ with a relative symlink to the real skill
+	mkdirSync(repoOpencodeSkills, { recursive: true })
+	symlinkSync("../../skills/category/my-skill", join(repoOpencodeSkills, "my-skill"))
+
+	// Create config/skills as an absolute symlink to .opencode/skills
+	mkdirSync(join(testDir, "config"), { recursive: true })
+	symlinkSync(repoOpencodeSkills, configSkills)
+})
+
+afterAll(() => {
+	rmSync(testDir, { recursive: true, force: true })
+})
+
+describe("resolveSymlink", () => {
+	it("resolves a regular file path to itself", () => {
+		const filePath = join(realSkillDir, "SKILL.md")
+		expect(resolveSymlink(filePath)).toBe(filePath)
+	})
+
+	it("resolves a relative symlink to its real path", () => {
+		const symlinkPath = join(repoOpencodeSkills, "my-skill")
+		expect(resolveSymlink(symlinkPath)).toBe(realSkillDir)
+	})
+
+	it("resolves a chained symlink (symlink-to-dir-containing-symlinks) to the real path", () => {
+		// This is the real-world scenario:
+		// config/skills/my-skill -> (follows config/skills) -> repo/.opencode/skills/my-skill -> repo/skills/category/my-skill
+		const chainedPath = join(configSkills, "my-skill")
+		expect(resolveSymlink(chainedPath)).toBe(realSkillDir)
+	})
+
+	it("returns the original path for non-existent paths", () => {
+		const fakePath = join(testDir, "does-not-exist")
+		expect(resolveSymlink(fakePath)).toBe(fakePath)
+	})
+})
+
+describe("resolveSymlinkAsync", () => {
+	it("resolves a regular file path to itself", async () => {
+		const filePath = join(realSkillDir, "SKILL.md")
+		expect(await resolveSymlinkAsync(filePath)).toBe(filePath)
+	})
+
+	it("resolves a relative symlink to its real path", async () => {
+		const symlinkPath = join(repoOpencodeSkills, "my-skill")
+		expect(await resolveSymlinkAsync(symlinkPath)).toBe(realSkillDir)
+	})
+
+	it("resolves a chained symlink (symlink-to-dir-containing-symlinks) to the real path", async () => {
+		const chainedPath = join(configSkills, "my-skill")
+		expect(await resolveSymlinkAsync(chainedPath)).toBe(realSkillDir)
+	})
+
+	it("returns the original path for non-existent paths", async () => {
+		const fakePath = join(testDir, "does-not-exist")
+		expect(await resolveSymlinkAsync(fakePath)).toBe(fakePath)
+	})
+})
+
+describe("isSymbolicLink", () => {
+	it("returns true for a symlink", () => {
+		expect(isSymbolicLink(join(repoOpencodeSkills, "my-skill"))).toBe(true)
+	})
+
+	it("returns false for a regular directory", () => {
+		expect(isSymbolicLink(realSkillDir)).toBe(false)
+	})
+
+	it("returns false for a non-existent path", () => {
+		expect(isSymbolicLink(join(testDir, "does-not-exist"))).toBe(false)
+	})
+})

src/shared/file-utils.ts

@@ -1,6 +1,5 @@
-import { lstatSync, readlinkSync } from "fs"
+import { lstatSync, realpathSync } from "fs"
 import { promises as fs } from "fs"
-import { resolve } from "path"
 
 export function isMarkdownFile(entry: { name: string; isFile: () => boolean }): boolean {
   return !entry.name.startsWith(".") && entry.name.endsWith(".md") && entry.isFile()
@@ -16,11 +15,7 @@ export function isSymbolicLink(filePath: string): boolean {
 
 export function resolveSymlink(filePath: string): string {
   try {
-    const stats = lstatSync(filePath, { throwIfNoEntry: false })
-    if (stats?.isSymbolicLink()) {
-      return resolve(filePath, "..", readlinkSync(filePath))
-    }
-    return filePath
+    return realpathSync(filePath)
   } catch {
     return filePath
   }
@@ -28,12 +23,7 @@ export function resolveSymlink(filePath: string): string {
 
 export async function resolveSymlinkAsync(filePath: string): Promise<string> {
   try {
-    const stats = await fs.lstat(filePath)
-    if (stats.isSymbolicLink()) {
-      const linkTarget = await fs.readlink(filePath)
-      return resolve(filePath, "..", linkTarget)
-    }
-    return filePath
+    return await fs.realpath(filePath)
   } catch {
     return filePath
   }

src/shared/session-tools-store.test.ts

@@ -0,0 +1,72 @@
+import { describe, test, expect, beforeEach } from "bun:test"
+import { setSessionTools, getSessionTools, clearSessionTools } from "./session-tools-store"
+
+describe("session-tools-store", () => {
+  beforeEach(() => {
+    clearSessionTools()
+  })
+
+  test("returns undefined for unknown session", () => {
+    //#given
+    const sessionID = "ses_unknown"
+
+    //#when
+    const result = getSessionTools(sessionID)
+
+    //#then
+    expect(result).toBeUndefined()
+  })
+
+  test("stores and retrieves tools for a session", () => {
+    //#given
+    const sessionID = "ses_abc123"
+    const tools = { question: false, task: true, call_omo_agent: true }
+
+    //#when
+    setSessionTools(sessionID, tools)
+    const result = getSessionTools(sessionID)
+
+    //#then
+    expect(result).toEqual({ question: false, task: true, call_omo_agent: true })
+  })
+
+  test("overwrites existing tools for same session", () => {
+    //#given
+    const sessionID = "ses_abc123"
+    setSessionTools(sessionID, { question: false })
+
+    //#when
+    setSessionTools(sessionID, { question: true, task: false })
+    const result = getSessionTools(sessionID)
+
+    //#then
+    expect(result).toEqual({ question: true, task: false })
+  })
+
+  test("clearSessionTools removes all entries", () => {
+    //#given
+    setSessionTools("ses_1", { question: false })
+    setSessionTools("ses_2", { task: true })
+
+    //#when
+    clearSessionTools()
+
+    //#then
+    expect(getSessionTools("ses_1")).toBeUndefined()
+    expect(getSessionTools("ses_2")).toBeUndefined()
+  })
+
+  test("returns a copy, not a reference", () => {
+    //#given
+    const sessionID = "ses_abc123"
+    const tools = { question: false }
+    setSessionTools(sessionID, tools)
+
+    //#when
+    const result = getSessionTools(sessionID)!
+    result.question = true
+
+    //#then
+    expect(getSessionTools(sessionID)).toEqual({ question: false })
+  })
+})

src/shared/session-tools-store.ts

@@ -0,0 +1,14 @@
+const store = new Map<string, Record<string, boolean>>()
+
+export function setSessionTools(sessionID: string, tools: Record<string, boolean>): void {
+  store.set(sessionID, { ...tools })
+}
+
+export function getSessionTools(sessionID: string): Record<string, boolean> | undefined {
+  const tools = store.get(sessionID)
+  return tools ? { ...tools } : undefined
+}
+
+export function clearSessionTools(): void {
+  store.clear()
+}

src/tools/call-omo-agent/background-agent-executor.ts

@@ -5,6 +5,7 @@ import { log } from "../../shared"
 import type { CallOmoAgentArgs } from "./types"
 import type { ToolContextWithMetadata } from "./tool-context-with-metadata"
 import { getMessageDir } from "./message-storage-directory"
+import { getSessionTools } from "../../shared/session-tools-store"
 
 export async function executeBackgroundAgent(
 	args: CallOmoAgentArgs,
@@ -36,6 +37,7 @@ export async function executeBackgroundAgent(
 			parentSessionID: toolContext.sessionID,
 			parentMessageID: toolContext.messageID,
 			parentAgent,
+			parentTools: getSessionTools(toolContext.sessionID),
 		})
 
 		const waitStart = Date.now()

src/tools/call-omo-agent/background-executor.ts

@@ -5,6 +5,7 @@ import { consumeNewMessages } from "../../shared/session-cursor"
 import { findFirstMessageWithAgent, findNearestMessageWithFields } from "../../features/hook-message-injector"
 import { getSessionAgent } from "../../features/claude-code-session-state"
 import { getMessageDir } from "./message-dir"
+import { getSessionTools } from "../../shared/session-tools-store"
 
 export async function executeBackground(
   args: CallOmoAgentArgs,
@@ -41,6 +42,7 @@ export async function executeBackground(
       parentSessionID: toolContext.sessionID,
       parentMessageID: toolContext.messageID,
       parentAgent,
+      parentTools: getSessionTools(toolContext.sessionID),
     })
 
     const WAIT_FOR_SESSION_INTERVAL_MS = 50

src/tools/call-omo-agent/sync-executor.test.ts

@@ -1,16 +1,28 @@
-const { describe, test, expect, mock } = require("bun:test")
+const { describe, test, expect, mock, beforeEach, afterEach } = require("bun:test")
 
-mock.module("./session-creator", () => ({
-  createOrGetSession: mock(async () => ({ sessionID: "ses-test-123" })),
-}))
+const realCompletionPoller = require("./completion-poller")
+const realMessageProcessor = require("./message-processor")
 
-mock.module("./completion-poller", () => ({
-  waitForCompletion: mock(async () => {}),
-}))
+const waitForCompletionMock = mock(async () => {})
+const processMessagesMock = mock(async () => "agent response")
 
-mock.module("./message-processor", () => ({
-  processMessages: mock(async () => "agent response"),
-}))
+beforeEach(() => {
+  waitForCompletionMock.mockClear()
+  processMessagesMock.mockClear()
+
+  mock.module("./completion-poller", () => ({
+    waitForCompletion: waitForCompletionMock,
+  }))
+
+  mock.module("./message-processor", () => ({
+    processMessages: processMessagesMock,
+  }))
+})
+
+afterEach(() => {
+  mock.module("./completion-poller", () => ({ ...realCompletionPoller }))
+  mock.module("./message-processor", () => ({ ...realMessageProcessor }))
+})
 
 describe("executeSync", () => {
   test("passes question=false via tools parameter to block question tool", async () => {
@@ -27,6 +39,7 @@ describe("executeSync", () => {
       subagent_type: "explore",
       description: "test task",
       prompt: "find something",
+      session_id: "ses-test-123",
     }
 
     const toolContext = {
@@ -39,7 +52,10 @@ describe("executeSync", () => {
 
     const ctx = {
       client: {
-        session: { promptAsync },
+        session: {
+          promptAsync,
+          get: mock(async () => ({ data: { id: "ses-test-123" } })),
+        },
       },
     }
 
@@ -65,6 +81,7 @@ describe("executeSync", () => {
       subagent_type: "librarian",
       description: "search docs",
       prompt: "find docs",
+      session_id: "ses-test-123",
     }
 
     const toolContext = {
@@ -77,7 +94,10 @@ describe("executeSync", () => {
 
     const ctx = {
       client: {
-        session: { promptAsync },
+        session: {
+          promptAsync,
+          get: mock(async () => ({ data: { id: "ses-test-123" } })),
+        },
       },
     }
 

src/tools/delegate-task/background-continuation.ts

@@ -2,6 +2,7 @@ import type { DelegateTaskArgs, ToolContextWithMetadata } from "./types"
 import type { ExecutorContext, ParentContext } from "./executor-types"
 import { storeToolMetadata } from "../../features/tool-metadata-store"
 import { formatDetailedError } from "./error-formatting"
+import { getSessionTools } from "../../shared/session-tools-store"
 
 export async function executeBackgroundContinuation(
   args: DelegateTaskArgs,
@@ -19,6 +20,7 @@ export async function executeBackgroundContinuation(
       parentMessageID: parentContext.messageID,
       parentModel: parentContext.model,
       parentAgent: parentContext.agent,
+      parentTools: getSessionTools(parentContext.sessionID),
     })
 
     const bgContMeta = {

src/tools/delegate-task/background-task.ts

@@ -3,6 +3,7 @@ import type { ExecutorContext, ParentContext } from "./executor-types"
 import { getTimingConfig } from "./timing"
 import { storeToolMetadata } from "../../features/tool-metadata-store"
 import { formatDetailedError } from "./error-formatting"
+import { getSessionTools } from "../../shared/session-tools-store"
 
 export async function executeBackgroundTask(
   args: DelegateTaskArgs,
@@ -24,6 +25,7 @@ export async function executeBackgroundTask(
       parentMessageID: parentContext.messageID,
       parentModel: parentContext.model,
       parentAgent: parentContext.agent,
+      parentTools: getSessionTools(parentContext.sessionID),
       model: categoryModel,
       skills: args.load_skills.length > 0 ? args.load_skills : undefined,
       skillContent: systemContent,

src/tools/delegate-task/sync-continuation.ts

@@ -9,6 +9,7 @@ import { promptWithModelSuggestionRetry } from "../../shared/model-suggestion-re
 import { findNearestMessageWithFields } from "../../features/hook-message-injector"
 import { formatDuration } from "./time-formatter"
 import { syncContinuationDeps, type SyncContinuationDeps } from "./sync-continuation-deps"
+import { setSessionTools } from "../../shared/session-tools-store"
 
 export async function executeSyncContinuation(
   args: DelegateTaskArgs,
@@ -77,6 +78,13 @@ export async function executeSyncContinuation(
     }
 
     const allowTask = isPlanFamily(resumeAgent)
+    const tools = {
+      ...(resumeAgent ? getAgentToolRestrictions(resumeAgent) : {}),
+      task: allowTask,
+      call_omo_agent: true,
+      question: false,
+    }
+    setSessionTools(args.session_id!, tools)
 
     await promptWithModelSuggestionRetry(client, {
       path: { id: args.session_id! },
@@ -84,12 +92,7 @@ export async function executeSyncContinuation(
         ...(resumeAgent !== undefined ? { agent: resumeAgent } : {}),
         ...(resumeModel !== undefined ? { model: resumeModel } : {}),
         ...(resumeVariant !== undefined ? { variant: resumeVariant } : {}),
-        tools: {
-          ...(resumeAgent ? getAgentToolRestrictions(resumeAgent) : {}),
-          task: allowTask,
-          call_omo_agent: true, // Intentionally overrides restrictions - continuation context needs delegation capability even for restricted agents
-          question: false,
-        },
+        tools,
         parts: [{ type: "text", text: args.prompt }],
       },
     })

src/tools/delegate-task/sync-prompt-sender.ts

@@ -3,6 +3,7 @@ import { isPlanFamily } from "./constants"
 import { promptWithModelSuggestionRetry } from "../../shared/model-suggestion-retry"
 import { formatDetailedError } from "./error-formatting"
 import { getAgentToolRestrictions } from "../../shared/agent-tool-restrictions"
+import { setSessionTools } from "../../shared/session-tools-store"
 
 export async function sendSyncPrompt(
   client: OpencodeClient,
@@ -18,17 +19,19 @@ export async function sendSyncPrompt(
 ): Promise<string | null> {
   try {
     const allowTask = isPlanFamily(input.agentToUse)
+    const tools = {
+      task: allowTask,
+      call_omo_agent: true,
+      question: false,
+      ...getAgentToolRestrictions(input.agentToUse),
+    }
+    setSessionTools(input.sessionID, tools)
     await promptWithModelSuggestionRetry(client, {
       path: { id: input.sessionID },
       body: {
         agent: input.agentToUse,
         system: input.systemContent,
-        tools: {
-          task: allowTask,
-          call_omo_agent: true,
-          question: false,
-          ...getAgentToolRestrictions(input.agentToUse),
-        },
+        tools,
         parts: [{ type: "text", text: input.args.prompt }],
         ...(input.categoryModel ? { model: { providerID: input.categoryModel.providerID, modelID: input.categoryModel.modelID } } : {}),
         ...(input.categoryModel?.variant ? { variant: input.categoryModel.variant } : {}),

src/tools/delegate-task/unstable-agent-task.ts

@@ -4,6 +4,7 @@ import { getTimingConfig } from "./timing"
 import { storeToolMetadata } from "../../features/tool-metadata-store"
 import { formatDuration } from "./time-formatter"
 import { formatDetailedError } from "./error-formatting"
+import { getSessionTools } from "../../shared/session-tools-store"
 
 export async function executeUnstableAgentTask(
   args: DelegateTaskArgs,
@@ -26,6 +27,7 @@ export async function executeUnstableAgentTask(
       parentMessageID: parentContext.messageID,
       parentModel: parentContext.model,
       parentAgent: parentContext.agent,
+      parentTools: getSessionTools(parentContext.sessionID),
       model: categoryModel,
       skills: args.load_skills.length > 0 ? args.load_skills : undefined,
       skillContent: systemContent,

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,