Problem

Cron jobs with kind: systemEvent were not being processed when HEARTBEAT.md was empty.

The heartbeat runner skips execution when HEARTBEAT.md has no actionable content to save API costs. However, only exec-event was exempted from this optimization, while cron jobs with pending system events were incorrectly skipped.

This caused system events from cron to queue up indefinitely until a user message triggered processing.

Solution

Add isCronReason check alongside isExecEventReason to prevent skipping heartbeat when cron jobs enqueue system events.

Changes

• Added check for cron reasons (opts.reason?.startsWith("cron:"))
• Updated condition to not skip heartbeat for cron-triggered events

Fixes #5349

Greptile Overview

Greptile Summary

This PR updates the heartbeat “empty HEARTBEAT.md” optimization in src/infra/heartbeat-runner.ts so that the runner will not skip heartbeats when the wake reason indicates a cron-triggered run (reason starts with cron:), alongside the existing exception for exec-event. This aligns the skip logic with the fact that cron systemEvent jobs may have pending system events to process even when the heartbeat file itself is effectively empty, preventing cron-enqueued events from stalling until a user message arrives.

Confidence Score: 5/5

• This PR is safe to merge with minimal risk.
• The change is small, localized, and consistent with existing reason-based exceptions, using a null-safe check for cron-prefixed reasons; it only broadens the set of reasons that bypass the empty-heartbeat skip, which matches the stated behavior for pending system events.
• No files require special attention

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