feat(core): pause agent timeout budget while waiting for tool confirmation

packages/core/src/agents/agent-scheduler.ts

@@ -27,6 +27,8 @@ export interface AgentSchedulingOptions {
   signal: AbortSignal;
   /** Optional function to get the preferred editor for tool modifications. */
   getPreferredEditor?: () => EditorType | undefined;
+  /** Optional function to be notified when the scheduler is waiting for user confirmation. */
+  onWaitingForConfirmation?: (waiting: boolean) => void;
 }
 
 /**
@@ -48,6 +50,7 @@ export async function scheduleAgentTools(
     toolRegistry,
     signal,
     getPreferredEditor,
+    onWaitingForConfirmation,
   } = options;
 
   // Create a proxy/override of the config to provide the agent-specific tool registry.
@@ -60,6 +63,7 @@ export async function scheduleAgentTools(
     getPreferredEditor: getPreferredEditor ?? (() => undefined),
     schedulerId,
     parentCallId,
+    onWaitingForConfirmation,
   });
 
   return scheduler.schedule(requests, signal);

packages/core/src/agents/local-executor.ts

@@ -58,6 +58,7 @@ import { getModelConfigAlias } from './registry.js';
 import { getVersion } from '../utils/version.js';
 import { getToolCallContext } from '../utils/toolCallContext.js';
 import { scheduleAgentTools } from './agent-scheduler.js';
+import { DeadlineTimer } from '../utils/deadlineTimer.js';
 
 /** A callback function to report on agent activity. */
 export type ActivityCallback = (activity: SubagentActivityEvent) => void;
@@ -231,6 +232,7 @@ export class LocalAgentExecutor<TOutput extends z.ZodTypeAny> {
     turnCounter: number,
     combinedSignal: AbortSignal,
     timeoutSignal: AbortSignal, // Pass the timeout controller's signal
+    onWaitingForConfirmation?: (waiting: boolean) => void,
   ): Promise<AgentTurnResult> {
     const promptId = `${this.agentId}#${turnCounter}`;
 
@@ -265,7 +267,12 @@ export class LocalAgentExecutor<TOutput extends z.ZodTypeAny> {
     }
 
     const { nextMessage, submittedOutput, taskCompleted } =
-      await this.processFunctionCalls(functionCalls, combinedSignal, promptId);
+      await this.processFunctionCalls(
+        functionCalls,
+        combinedSignal,
+        promptId,
+        onWaitingForConfirmation,
+      );
     if (taskCompleted) {
       const finalResult = submittedOutput ?? 'Task completed successfully.';
       return {
@@ -322,6 +329,7 @@ export class LocalAgentExecutor<TOutput extends z.ZodTypeAny> {
       | AgentTerminateMode.MAX_TURNS
       | AgentTerminateMode.ERROR_NO_COMPLETE_TASK_CALL,
     externalSignal: AbortSignal, // The original signal passed to run()
+    onWaitingForConfirmation?: (waiting: boolean) => void,
   ): Promise<string | null> {
     this.emitActivity('THOUGHT_CHUNK', {
       text: `Execution limit reached (${reason}). Attempting one final recovery turn with a grace period.`,
@@ -355,6 +363,7 @@ export class LocalAgentExecutor<TOutput extends z.ZodTypeAny> {
         turnCounter, // This will be the "last" turn number
         combinedSignal,
         graceTimeoutController.signal, // Pass grace signal to identify a *grace* timeout
+        onWaitingForConfirmation,
       );
 
       if (
@@ -415,14 +424,22 @@ export class LocalAgentExecutor<TOutput extends z.ZodTypeAny> {
       this.definition.runConfig.maxTimeMinutes ?? DEFAULT_MAX_TIME_MINUTES;
     const maxTurns = this.definition.runConfig.maxTurns ?? DEFAULT_MAX_TURNS;
 
-    const timeoutController = new AbortController();
-    const timeoutId = setTimeout(
-      () => timeoutController.abort(new Error('Agent timed out.')),
+    const deadlineTimer = new DeadlineTimer(
       maxTimeMinutes * 60 * 1000,
+      'Agent timed out.',
     );
 
+    // Track time spent waiting for user confirmation to credit it back to the agent.
+    const onWaitingForConfirmation = (waiting: boolean) => {
+      if (waiting) {
+        deadlineTimer.pause();
+      } else {
+        deadlineTimer.resume();
+      }
+    };
+
     // Combine the external signal with the internal timeout signal.
-    const combinedSignal = AbortSignal.any([signal, timeoutController.signal]);
+    const combinedSignal = AbortSignal.any([signal, deadlineTimer.signal]);
 
     logAgentStart(
       this.runtimeContext,
@@ -458,7 +475,7 @@ export class LocalAgentExecutor<TOutput extends z.ZodTypeAny> {
         // Check for timeout or external abort.
         if (combinedSignal.aborted) {
           // Determine which signal caused the abort.
-          terminateReason = timeoutController.signal.aborted
+          terminateReason = deadlineTimer.signal.aborted
             ? AgentTerminateMode.TIMEOUT
             : AgentTerminateMode.ABORTED;
           break;
@@ -469,7 +486,8 @@ export class LocalAgentExecutor<TOutput extends z.ZodTypeAny> {
           currentMessage,
           turnCounter++,
           combinedSignal,
-          timeoutController.signal,
+          deadlineTimer.signal,
+          onWaitingForConfirmation,
         );
 
         if (turnResult.status === 'stop') {
@@ -498,6 +516,7 @@ export class LocalAgentExecutor<TOutput extends z.ZodTypeAny> {
           turnCounter, // Use current turnCounter for the recovery attempt
           terminateReason,
           signal, // Pass the external signal
+          onWaitingForConfirmation,
         );
 
         if (recoveryResult !== null) {
@@ -551,7 +570,7 @@ export class LocalAgentExecutor<TOutput extends z.ZodTypeAny> {
       if (
         error instanceof Error &&
         error.name === 'AbortError' &&
-        timeoutController.signal.aborted &&
+        deadlineTimer.signal.aborted &&
         !signal.aborted // Ensure the external signal was not the cause
       ) {
         terminateReason = AgentTerminateMode.TIMEOUT;
@@ -563,6 +582,7 @@ export class LocalAgentExecutor<TOutput extends z.ZodTypeAny> {
             turnCounter, // Use current turnCounter
             AgentTerminateMode.TIMEOUT,
             signal,
+            onWaitingForConfirmation,
           );
 
           if (recoveryResult !== null) {
@@ -591,7 +611,7 @@ export class LocalAgentExecutor<TOutput extends z.ZodTypeAny> {
       this.emitActivity('ERROR', { error: String(error) });
       throw error; // Re-throw other errors or external aborts.
     } finally {
-      clearTimeout(timeoutId);
+      deadlineTimer.abort();
       logAgentFinish(
         this.runtimeContext,
         new AgentFinishEvent(
@@ -779,6 +799,7 @@ export class LocalAgentExecutor<TOutput extends z.ZodTypeAny> {
     functionCalls: FunctionCall[],
     signal: AbortSignal,
     promptId: string,
+    onWaitingForConfirmation?: (waiting: boolean) => void,
   ): Promise<{
     nextMessage: Content;
     submittedOutput: string | null;
@@ -979,6 +1000,7 @@ export class LocalAgentExecutor<TOutput extends z.ZodTypeAny> {
           parentCallId: this.parentCallId,
           toolRegistry: this.toolRegistry,
           signal,
+          onWaitingForConfirmation,
         },
       );
 

packages/core/src/scheduler/confirmation.ts

@@ -104,9 +104,10 @@ export async function resolveConfirmation(
     modifier: ToolModificationHandler;
     getPreferredEditor: () => EditorType | undefined;
     schedulerId: string;
+    onWaitingForConfirmation?: (waiting: boolean) => void;
   },
 ): Promise<ResolutionResult> {
-  const { state } = deps;
+  const { state, onWaitingForConfirmation } = deps;
   const callId = toolCall.request.callId;
   let outcome = ToolConfirmationOutcome.ModifyWithEditor;
   let lastDetails: SerializableConfirmationDetails | undefined;
@@ -142,12 +143,14 @@ export async function resolveConfirmation(
       correlationId,
     });
 
+    onWaitingForConfirmation?.(true);
     const response = await waitForConfirmation(
       deps.messageBus,
       correlationId,
       signal,
       ideConfirmation,
     );
+    onWaitingForConfirmation?.(false);
     outcome = response.outcome;
 
     if ('onConfirm' in details && typeof details.onConfirm === 'function') {

packages/core/src/scheduler/scheduler.ts

@@ -51,6 +51,7 @@ export interface SchedulerOptions {
   getPreferredEditor: () => EditorType | undefined;
   schedulerId: string;
   parentCallId?: string;
+  onWaitingForConfirmation?: (waiting: boolean) => void;
 }
 
 const createErrorResponse = (
@@ -90,6 +91,7 @@ export class Scheduler {
   private readonly getPreferredEditor: () => EditorType | undefined;
   private readonly schedulerId: string;
   private readonly parentCallId?: string;
+  private readonly onWaitingForConfirmation?: (waiting: boolean) => void;
 
   private isProcessing = false;
   private isCancelling = false;
@@ -101,6 +103,7 @@ export class Scheduler {
     this.getPreferredEditor = options.getPreferredEditor;
     this.schedulerId = options.schedulerId;
     this.parentCallId = options.parentCallId;
+    this.onWaitingForConfirmation = options.onWaitingForConfirmation;
     this.state = new SchedulerStateManager(
       this.messageBus,
       this.schedulerId,
@@ -437,6 +440,7 @@ export class Scheduler {
         modifier: this.modifier,
         getPreferredEditor: this.getPreferredEditor,
         schedulerId: this.schedulerId,
+        onWaitingForConfirmation: this.onWaitingForConfirmation,
       });
       outcome = result.outcome;
       lastDetails = result.lastDetails;

packages/core/src/scheduler/scheduler_waiting_callback.test.ts

@@ -0,0 +1,80 @@
+/**
+ * @license
+ * Copyright 2026 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { describe, it, expect, vi, beforeEach } from 'vitest';
+import { Scheduler } from './scheduler.js';
+import { resolveConfirmation } from './confirmation.js';
+import { checkPolicy } from './policy.js';
+import { PolicyDecision } from '../policy/types.js';
+import { ToolConfirmationOutcome } from '../tools/tools.js';
+import { ToolRegistry } from '../tools/tool-registry.js';
+import { MockTool } from '../test-utils/mock-tool.js';
+import { createMockMessageBus } from '../test-utils/mock-message-bus.js';
+import { makeFakeConfig } from '../test-utils/config.js';
+import type { Config } from '../config/config.js';
+import type { ToolCallRequestInfo } from './types.js';
+import type { MessageBus } from '../confirmation-bus/message-bus.js';
+
+vi.mock('./confirmation.js');
+vi.mock('./policy.js');
+
+describe('Scheduler waiting callback', () => {
+  let mockConfig: Config;
+  let messageBus: MessageBus;
+  let toolRegistry: ToolRegistry;
+  let mockTool: MockTool;
+
+  beforeEach(() => {
+    messageBus = createMockMessageBus();
+    mockConfig = makeFakeConfig();
+
+    // Override methods to use our mocks
+    vi.spyOn(mockConfig, 'getMessageBus').mockReturnValue(messageBus);
+
+    mockTool = new MockTool({ name: 'test_tool' });
+    toolRegistry = new ToolRegistry(mockConfig, messageBus);
+    vi.spyOn(mockConfig, 'getToolRegistry').mockReturnValue(toolRegistry);
+    toolRegistry.registerTool(mockTool);
+
+    vi.mocked(checkPolicy).mockResolvedValue({
+      decision: PolicyDecision.ASK_USER,
+      rule: undefined,
+    });
+  });
+
+  it('should trigger onWaitingForConfirmation callback', async () => {
+    const onWaitingForConfirmation = vi.fn();
+    const scheduler = new Scheduler({
+      config: mockConfig,
+      messageBus,
+      getPreferredEditor: () => undefined,
+      schedulerId: 'test-scheduler',
+      onWaitingForConfirmation,
+    });
+
+    vi.mocked(resolveConfirmation).mockResolvedValue({
+      outcome: ToolConfirmationOutcome.ProceedOnce,
+    });
+
+    const req: ToolCallRequestInfo = {
+      callId: 'call-1',
+      name: 'test_tool',
+      args: {},
+      isClientInitiated: false,
+      prompt_id: 'test-prompt',
+    };
+
+    await scheduler.schedule(req, new AbortController().signal);
+
+    expect(resolveConfirmation).toHaveBeenCalledWith(
+      expect.anything(),
+      expect.anything(),
+      expect.objectContaining({
+        onWaitingForConfirmation,
+      }),
+    );
+  });
+});

packages/core/src/utils/deadlineTimer.test.ts

@@ -0,0 +1,82 @@
+/**
+ * @license
+ * Copyright 2026 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest';
+import { DeadlineTimer } from './deadlineTimer.js';
+
+describe('DeadlineTimer', () => {
+  beforeEach(() => {
+    vi.useFakeTimers();
+  });
+
+  afterEach(() => {
+    vi.restoreAllMocks();
+  });
+
+  it('should abort when timeout is reached', () => {
+    const timer = new DeadlineTimer(1000);
+    const signal = timer.signal;
+    expect(signal.aborted).toBe(false);
+
+    vi.advanceTimersByTime(1000);
+    expect(signal.aborted).toBe(true);
+    expect(signal.reason).toBeInstanceOf(Error);
+    expect((signal.reason as Error).message).toBe('Timeout exceeded.');
+  });
+
+  it('should allow extending the deadline', () => {
+    const timer = new DeadlineTimer(1000);
+    const signal = timer.signal;
+
+    vi.advanceTimersByTime(500);
+    expect(signal.aborted).toBe(false);
+
+    timer.extend(1000); // New deadline is 1000 + 1000 = 2000 from start
+
+    vi.advanceTimersByTime(600); // 1100 total
+    expect(signal.aborted).toBe(false);
+
+    vi.advanceTimersByTime(900); // 2000 total
+    expect(signal.aborted).toBe(true);
+  });
+
+  it('should allow pausing and resuming the timer', () => {
+    const timer = new DeadlineTimer(1000);
+    const signal = timer.signal;
+
+    vi.advanceTimersByTime(500);
+    timer.pause();
+
+    vi.advanceTimersByTime(2000); // Wait a long time while paused
+    expect(signal.aborted).toBe(false);
+
+    timer.resume();
+    vi.advanceTimersByTime(400);
+    expect(signal.aborted).toBe(false);
+
+    vi.advanceTimersByTime(200); // Total active time 500 + 400 + 200 = 1100
+    expect(signal.aborted).toBe(true);
+  });
+
+  it('should abort immediately when abort() is called', () => {
+    const timer = new DeadlineTimer(1000);
+    const signal = timer.signal;
+
+    timer.abort('cancelled');
+    expect(signal.aborted).toBe(true);
+    expect(signal.reason).toBe('cancelled');
+  });
+
+  it('should not fire timeout if aborted manually', () => {
+    const timer = new DeadlineTimer(1000);
+    const signal = timer.signal;
+
+    timer.abort();
+    vi.advanceTimersByTime(1000);
+    // Already aborted, but shouldn't re-abort or throw
+    expect(signal.aborted).toBe(true);
+  });
+});