[BUG] Queued ScheduleWakeup silently dropped when a background Agent completion (or macOS sleep/wake) re-enters the session

TL;DR

A pending ScheduleWakeup is silently dropped when its target time elapses while a background Agent (Agent tool, run_in_background: true) is still running. The session stays alive — the wakeup is not lost to a crash. Instead it appears to be absorbed by the Agent-completion notification path: when the background Agent finishes, its task-notification re-invokes the session, and the queued wakeup that should have fired during the Agent's run never fires.

A likely-related variant (same symptom, distinct trigger): a queued wakeup is also dropped across a macOS system sleep — the session survives the sleep/wake cycle but its self-paced loop never resumes, with no background Agent involved.

Impact: this silently ends a self-paced ScheduleWakeup loop. A swallowed reschedule means the next tick never happens, so the loop dies with no error and no user-visible signal.

Environment

• Claude Code 2.1.197
• VSCode extension
• macOS (Darwin 25.5.0)

Reproduction — background-Agent trigger

1. Start a self-paced ScheduleWakeup loop (each turn schedules the next wakeup).
2. On some turn, also spawn a background Agent (Agent tool with run_in_background: true) whose runtime spans the next wakeup's target time.
3. The harness confirms Next wakeup scheduled for ….
4. The wakeup's target time passes while the Agent is still running — no fire.
5. The Agent completes; its task-notification re-invokes the session.
6. Observed: the queued wakeup never fired on its own; it is absorbed into the notification re-entry. The self-paced loop, which relied on that fire to reschedule, silently ends.

Transcript evidence (reproduced 2×)

• (i) 02:57Z turn → 03:02Z wakeup target. No fire until a 03:16Z Agent-completion notification.
• (ii) 04:07Z turn → 04:12Z wakeup target. No fire until 04:23Z.

In both cases the wakeup target elapsed mid-Agent-run and never fired independently.

Reproduction — sleep/wake variant (possibly same root cause)

1. Start a self-paced ScheduleWakeup loop. No background Agent involved.
2. Put the Mac to sleep spanning the next wakeup target (observed ~04:28–06:28Z).
3. Wake the Mac. The session is still alive.
4. Observed: the self-paced loop never resumes; the queued wakeup that came due during sleep never fires.

Expected

A queued ScheduleWakeup should fire on its own schedule (or fire promptly on the next re-entry) regardless of a concurrent background-Agent completion or a sleep/wake cycle. It should not be silently absorbed by the notification re-entry path.

Hypothesis

Both symptoms point to a single queued-wakeup timer that only one wake path can consume: an Agent-completion task-notification (or a sleep/wake resume) re-enters the session and clears/consumes the pending wakeup without firing it, so the loop's reschedule step never runs.

Timestamps + full transcripts available on request.