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

[Saikrishna1876]

Summary

This PR fixes issue #1069 where the "Working..." timer continued to count even while the agent was waiting for user input.

Changes:

• UI Logic: Updated isWorking state in ChatView to exclude phases where the agent is waiting for user input.
• Duration Calculation: Implemented formatTurnWorkElapsedExcludingUserInputWait helper to accurately calculate "Worked for" duration by subtracting intervals spent waiting for user feedback.
• Stability: Increased timeouts for app-server and test suites to prevent flakiness during long-running operations.

Verification:

• Video 1 (Agent stops counting when user is asked a question):
  /Users/saikrishnaambeti/Documents/Screenshots/Screen Screen Recording 2026-03-14 at 17.36.11.mov
• Video 2 (Normal working of the timer when agent is working):
  /Users/saikrishnaambeti/Documents/Screenshots/Screen Screen Recording 2026-03-14 at 17.36.44.mov

This PR adheres to the @CONTRIBUTING.md guidelines:

• Small, focused bug fix.
• Tightly scoped maintenance.
• Includes video evidence for timing/interaction changes.

Note

Fix timer to stop counting while waiting for user input

• Adds deriveUserInputWaitIntervals and formatTurnWorkElapsedExcludingUserInputWait to session-logic.ts to compute and format working time with user-input wait periods subtracted.
• Updates ChatView.tsx to pause the live timer when waiting for user input and to display elapsed time excluding wait durations.
• Adds a 'waiting' row variant to MessagesTimeline.tsx that renders an animated 'Waiting for you' indicator when the agent is blocked on user input.
• Behavioral Change: the working timer now pauses (rather than continues ticking) while the agent is waiting for user input, and the elapsed time shown in completion summaries excludes user-input wait durations.

^{Macroscope summarized a52aa83.}

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[chatgpt-codex-connector]

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[Saikrishna1876]

Screen.Recording.2026-03-14.at.17.36.44.mov

Agent working normally and it's time is being counted. ☝️

Screen.Recording.2026-03-14.at.17.36.11.mov

Agent is waiting for the user and the time counter is paused. ☝️