fix: timer stops counting when waiting for user input (#1069)

apps/server/src/codexAppServerManager.ts

@@ -164,6 +164,8 @@ const RECOVERABLE_THREAD_RESUME_ERROR_SNIPPETS = [
 const CODEX_DEFAULT_MODEL = "gpt-5.3-codex";
 const CODEX_SPARK_MODEL = "gpt-5.3-codex-spark";
 const CODEX_SPARK_DISABLED_PLAN_TYPES = new Set<CodexPlanType>(["free", "go", "plus"]);
+const CODEX_LONG_RUNNING_TOOL_TIMEOUT_SEC = 315_360_000;
+const CODEX_LONG_RUNNING_STREAM_IDLE_TIMEOUT_MS = 315_360_000_000;
 
 function asObject(value: unknown): Record<string, unknown> | undefined {
   if (!value || typeof value !== "object") {
@@ -548,15 +550,25 @@ export class CodexAppServerManager extends EventEmitter<CodexAppServerManagerEve
         cwd: resolvedCwd,
         ...(codexHomePath ? { homePath: codexHomePath } : {}),
       });
-      const child = spawn(codexBinaryPath, ["app-server"], {
-        cwd: resolvedCwd,
-        env: {
-          ...process.env,
-          ...(codexHomePath ? { CODEX_HOME: codexHomePath } : {}),
+      const child = spawn(
+        codexBinaryPath,
+        [
+          "app-server",
+          "-c",
+          `tool_timeout_sec=${CODEX_LONG_RUNNING_TOOL_TIMEOUT_SEC}`,
+          "-c",
+          `model_providers.openai.stream_idle_timeout_ms=${CODEX_LONG_RUNNING_STREAM_IDLE_TIMEOUT_MS}`,
+        ],
+        {
+          cwd: resolvedCwd,
+          env: {
+            ...process.env,
+            ...(codexHomePath ? { CODEX_HOME: codexHomePath } : {}),
+          },
+          stdio: ["pipe", "pipe", "pipe"],
+          shell: process.platform === "win32",
         },
-        stdio: ["pipe", "pipe", "pipe"],
-        shell: process.platform === "win32",
-      });
+      );
       const output = readline.createInterface({ input: child.stdout });
 
       context = {

apps/server/src/git/Layers/GitCore.test.ts

@@ -539,12 +539,15 @@ it.layer(TestLayer)("git integration", (it) => {
         yield* checkoutGitBranch({ cwd: source, branch: featureBranch });
         const core = yield* GitCore;
         yield* Effect.promise(() =>
-          vi.waitFor(async () => {
-            const details = await Effect.runPromise(core.statusDetails(source));
-            expect(details.branch).toBe(featureBranch);
-            expect(details.aheadCount).toBe(0);
-            expect(details.behindCount).toBe(1);
-          }),
+          vi.waitFor(
+            async () => {
+              const details = await Effect.runPromise(core.statusDetails(source));
+              expect(details.branch).toBe(featureBranch);
+              expect(details.aheadCount).toBe(0);
+              expect(details.behindCount).toBe(1);
+            },
+            { timeout: 10_000 },
+          ),
         );
       }),
     );

apps/server/src/orchestration/Layers/CheckpointReactor.test.ts

@@ -862,7 +862,7 @@ describe("CheckpointReactor", () => {
       }),
     );
 
-    const deadline = Date.now() + 2000;
+    const deadline = Date.now() + 10_000;
     const waitForRollbackCalls = async (): Promise<void> => {
       if (harness.provider.rollbackConversation.mock.calls.length >= 2) {
         return;

apps/server/vitest.config.ts

@@ -6,8 +6,8 @@ export default mergeConfig(
   baseConfig,
   defineConfig({
     test: {
-      testTimeout: 15_000,
-      hookTimeout: 15_000,
+      testTimeout: 240_000,
+      hookTimeout: 60_000,
     },
   }),
 );

apps/web/public/mockServiceWorker.js

@@ -7,7 +7,7 @@
  * - Please do NOT modify this file.
  */
 
-const PACKAGE_VERSION = '2.12.9'
+const PACKAGE_VERSION = '2.12.10'
 const INTEGRITY_CHECKSUM = '4db4a41e972cec1b64cc569c66952d82'
 const IS_MOCKED_RESPONSE = Symbol('isMockedResponse')
 const activeClientIds = new Set()

apps/web/src/components/ChatView.tsx

@@ -58,6 +58,7 @@ import {
   hasToolActivityForTurn,
   isLatestTurnSettled,
   formatElapsed,
+  formatTurnWorkElapsedExcludingUserInputWait,
 } from "../session-logic";
 import { isScrollContainerNearBottom } from "../chat-scroll";
 import {
@@ -568,7 +569,6 @@ export default function ChatView({ threadId }: ChatViewProps) {
   const phase = derivePhase(activeThread?.session ?? null);
   const isSendBusy = sendPhase !== "idle";
   const isPreparingWorktree = sendPhase === "preparing-worktree";
-  const isWorking = phase === "running" || isSendBusy || isConnecting || isRevertingCheckpoint;
   const nowIso = new Date(nowTick).toISOString();
   const activeWorkStartedAt = deriveActiveWorkStartedAt(
     activeLatestTurn,
@@ -593,6 +593,10 @@ export default function ChatView({ threadId }: ChatViewProps) {
     [threadActivities],
   );
   const activePendingUserInput = pendingUserInputs[0] ?? null;
+  const isWaitingForUserInput = activePendingUserInput !== null;
+  const isWorking =
+    (phase === "running" || isSendBusy || isConnecting || isRevertingCheckpoint) &&
+    !isWaitingForUserInput;
   const activePendingDraftAnswers = useMemo(
     () =>
       activePendingUserInput
@@ -862,14 +866,27 @@ export default function ChatView({ threadId }: ChatViewProps) {
     if (!activeLatestTurn.completedAt) return null;
     if (!latestTurnHasToolActivity) return null;
 
-    const elapsed = formatElapsed(activeLatestTurn.startedAt, activeLatestTurn.completedAt);
+    const elapsed = formatTurnWorkElapsedExcludingUserInputWait(
+      activeLatestTurn.startedAt,
+      activeLatestTurn.completedAt,
+      threadActivities,
+    );
     return elapsed ? `Worked for ${elapsed}` : null;
   }, [
     activeLatestTurn?.completedAt,
     activeLatestTurn?.startedAt,
     latestTurnHasToolActivity,
     latestTurnSettled,
+    threadActivities,
   ]);
+  const workingForLabel = useMemo(() => {
+    if (!isWorking) return null;
+    if (!activeWorkStartedAt) return null;
+    return (
+      formatTurnWorkElapsedExcludingUserInputWait(activeWorkStartedAt, nowIso, threadActivities) ??
+      formatElapsed(activeWorkStartedAt, nowIso)
+    );
+  }, [activeWorkStartedAt, isWorking, nowIso, threadActivities]);
   const completionDividerBeforeEntryId = useMemo(() => {
     if (!latestTurnSettled) return null;
     if (!activeLatestTurn?.startedAt) return null;
@@ -1900,14 +1917,14 @@ export default function ChatView({ threadId }: ChatViewProps) {
       : "local";
 
   useEffect(() => {
-    if (phase !== "running") return;
+    if (phase !== "running" || isWaitingForUserInput) return;
     const timer = window.setInterval(() => {
       setNowTick(Date.now());
     }, 1000);
     return () => {
       window.clearInterval(timer);
     };
-  }, [phase]);
+  }, [isWaitingForUserInput, phase]);
 
   const beginSendPhase = useCallback((nextPhase: Exclude<SendPhase, "idle">) => {
     setSendStartedAt((current) => current ?? new Date().toISOString());
@@ -3278,6 +3295,9 @@ export default function ChatView({ threadId }: ChatViewProps) {
               key={activeThread.id}
               hasMessages={timelineEntries.length > 0}
               isWorking={isWorking}
+              isWaitingForUserInput={isWaitingForUserInput}
+              waitingStartedAt={activePendingUserInput?.createdAt ?? null}
+              workingForLabel={workingForLabel}
               activeTurnInProgress={isWorking || !latestTurnSettled}
               activeTurnStartedAt={activeWorkStartedAt}
               scrollContainer={messagesScrollElement}

apps/web/src/components/chat/MessagesTimeline.tsx

@@ -43,6 +43,9 @@ const ALWAYS_UNVIRTUALIZED_TAIL_ROWS = 8;
 interface MessagesTimelineProps {
   hasMessages: boolean;
   isWorking: boolean;
+  isWaitingForUserInput: boolean;
+  waitingStartedAt: string | null;
+  workingForLabel: string | null;
   activeTurnInProgress: boolean;
   activeTurnStartedAt: string | null;
   scrollContainer: HTMLDivElement | null;
@@ -67,6 +70,9 @@ interface MessagesTimelineProps {
 export const MessagesTimeline = memo(function MessagesTimeline({
   hasMessages,
   isWorking,
+  isWaitingForUserInput,
+  waitingStartedAt,
+  workingForLabel,
   activeTurnInProgress,
   activeTurnStartedAt,
   scrollContainer,
@@ -113,7 +119,7 @@ export const MessagesTimeline = memo(function MessagesTimeline({
     return () => {
       observer.disconnect();
     };
-  }, [hasMessages, isWorking]);
+  }, [hasMessages, isWorking, isWaitingForUserInput]);
 
   const rows = useMemo<TimelineRow[]>(() => {
     const nextRows: TimelineRow[] = [];
@@ -175,10 +181,23 @@ export const MessagesTimeline = memo(function MessagesTimeline({
         id: "working-indicator-row",
         createdAt: activeTurnStartedAt,
       });
+    } else if (isWaitingForUserInput) {
+      nextRows.push({
+        kind: "waiting",
+        id: "waiting-indicator-row",
+        createdAt: waitingStartedAt ?? activeTurnStartedAt,
+      });
     }
 
     return nextRows;
-  }, [timelineEntries, completionDividerBeforeEntryId, isWorking, activeTurnStartedAt]);
+  }, [
+    timelineEntries,
+    completionDividerBeforeEntryId,
+    isWorking,
+    activeTurnStartedAt,
+    isWaitingForUserInput,
+    waitingStartedAt,
+  ]);
 
   const firstUnvirtualizedRowIndex = useMemo(() => {
     const firstTailRowIndex = Math.max(rows.length - ALWAYS_UNVIRTUALIZED_TAIL_ROWS, 0);
@@ -189,7 +208,7 @@ export const MessagesTimeline = memo(function MessagesTimeline({
     let firstCurrentTurnRowIndex = -1;
     if (!Number.isNaN(turnStartedAtMs)) {
       firstCurrentTurnRowIndex = rows.findIndex((row) => {
-        if (row.kind === "working") return true;
+        if (row.kind === "working" || row.kind === "waiting") return true;
         if (!row.createdAt) return false;
         const rowCreatedAtMs = Date.parse(row.createdAt);
         return !Number.isNaN(rowCreatedAtMs) && rowCreatedAtMs >= turnStartedAtMs;
@@ -233,7 +252,7 @@ export const MessagesTimeline = memo(function MessagesTimeline({
       if (!row) return 96;
       if (row.kind === "work") return 112;
       if (row.kind === "proposed-plan") return estimateTimelineProposedPlanHeight(row.proposedPlan);
-      if (row.kind === "working") return 40;
+      if (row.kind === "working" || row.kind === "waiting") return 40;
       return estimateTimelineMessageHeight(row.message, { timelineWidthPx });
     },
     measureElement: measureVirtualElement,
@@ -518,17 +537,32 @@ export const MessagesTimeline = memo(function MessagesTimeline({
               <span className="h-1 w-1 rounded-full bg-muted-foreground/30 animate-pulse [animation-delay:400ms]" />
             </span>
             <span>
-              {row.createdAt
-                ? `Working for ${formatWorkingTimer(row.createdAt, nowIso) ?? "0s"}`
-                : "Working..."}
+              {workingForLabel
+                ? `Working for ${workingForLabel}`
+                : row.createdAt
+                  ? `Working for ${formatWorkingTimer(row.createdAt, nowIso) ?? "0s"}`
+                  : "Working..."}
+            </span>
+          </div>
+        </div>
+      )}
+
+      {row.kind === "waiting" && (
+        <div className="py-0.5 pl-1.5">
+          <div className="flex items-center gap-2 pt-1 text-[11px] text-muted-foreground/70">
+            <span className="inline-flex items-center gap-[3px]">
+              <span className="h-1 w-1 rounded-full bg-muted-foreground/30 animate-pulse" />
+              <span className="h-1 w-1 rounded-full bg-muted-foreground/30 animate-pulse [animation-delay:200ms]" />
+              <span className="h-1 w-1 rounded-full bg-muted-foreground/30 animate-pulse [animation-delay:400ms]" />
             </span>
+            <span>Waiting for you</span>
           </div>
         </div>
       )}
     </div>
   );
 
-  if (!hasMessages && !isWorking) {
+  if (!hasMessages && !isWorking && !isWaitingForUserInput) {
     return (
       <div className="flex h-full items-center justify-center">
         <p className="text-sm text-muted-foreground/30">
@@ -597,7 +631,8 @@ type TimelineRow =
       createdAt: string;
       proposedPlan: TimelineProposedPlan;
     }
-  | { kind: "working"; id: string; createdAt: string | null };
+  | { kind: "working"; id: string; createdAt: string | null }
+  | { kind: "waiting"; id: string; createdAt: string | null };
 
 function estimateTimelineProposedPlanHeight(proposedPlan: TimelineProposedPlan): number {
   const estimatedLines = Math.max(1, Math.ceil(proposedPlan.planMarkdown.length / 72));