Add session and RLM heartbeats

[sethkarten]

Summary

• add a single combined heartbeat feature set for coding-agent sessions
• add persistent user-owned /heartbeat support with /heartbeat, /heartbeat pause, /heartbeat resume, and /heartbeat clear
• keep the user-level heartbeat user-controlled: models can inspect it with read-only get_heartbeat, but cannot create, update, pause, resume, clear, delete, or replace it through model tools
• add a bundled rlm-heartbeat Python skill exposed as await rlm_heartbeat.* from IPython
• back the RLM skill with rlm_heartbeat.list/create/update/delete host requests
• keep RLM heartbeats scoped by active session and separate from the user-level /heartbeat
• support multiple simultaneous RLM heartbeats with optional labels
• provide the RLM heartbeat controller to top-level daemon sessions, main-agent sessions, and RLM subagent sessions
• fix daemon-created runtime sessions so the RLM heartbeat controller is preserved when session options are resolved
• add regression coverage for user heartbeat lifecycle, controller propagation, deleted RLM heartbeats not firing after cancellation, and user-heartbeat model-tool immutability

Testing

• npx tsx ../../node_modules/vitest/dist/cli.js --run test/cron-jobs.test.ts test/kernel-rlm-heartbeat-skill.test.ts test/builtin-skills.test.ts test/slash-commands.test.ts test/daemon-command.test.ts test/agent-connection-daemon.test.ts test/main-interactive-routing.test.ts from packages/coding-agent — 95 tests passed
• npx tsgo --noEmit --pretty false
• npx tsx ../../node_modules/vitest/dist/cli.js --run from packages/coding-agent — 165 files passed, 1672 tests passed, 6 files skipped
• npm run check
• pre-commit npm run check on commits a3ecfcc1, 74a19ec3, and merge commit 0d360c06

Live validation

• launched pa-heartbeat-test through the full Prime Agent CLI/TUI entrypoint: ./prime-agent.sh --daemon-socket /tmp/pa-heartbeat-test.sock --provider prime-inference --model glm-5.1
• verified model-visible tools in the live session are ipython and read-only get_heartbeat; create_heartbeat and update_heartbeat are not available
• verified model-side attempts to access user-heartbeat mutation host requests are unavailable
• verified user-owned TUI slash lifecycle externally from the TUI: /heartbeat --every 5m ... created an active user heartbeat, /heartbeat pause changed it to paused, /heartbeat resume changed it back to active, and /heartbeat clear cancelled it; daemon queue then reported No cron jobs
• verified RLM skill can create, list, pause, resume, update, and delete multiple RLM-owned heartbeats from a live agent session
• verified deleted RLM heartbeats did not fire and remained separate from the user-level heartbeat
• verified parent and subagent RLM heartbeats use separate activeSessionId scopes: parent lists did not include child heartbeats, child lists did not include parent heartbeats, and cross-scope update/delete attempts returned null/no-op
• cleaned up live test jobs after validation; active daemon queue ended with No cron jobs

PR status

• single heartbeat draft PR directly against main
• supersedes feat(coding-agent): add persistent session heartbeat #165
• comments/reviews on this PR: one Macroscope low-severity inline review comment fixed in 05b4edd
• review threads on this PR: one Macroscope low-severity thread fixed in 05b4edd and resolved

Note

Add session and RLM heartbeats with daemon-backed cron job scheduling

• Introduces a cron job and heartbeat system to the daemon (daemon-mode.ts, cron-jobs.ts) that persists scheduled prompts to cron-jobs.json and dispatches them against long-running sessions.
• Adds daemon RPC commands cron_list, cron_add, cron_cancel, heartbeat_get, heartbeat_set, heartbeat_update to the protocol and CLI (daemon cron list/add/cancel).
• Adds a rlm-heartbeat Python skill that lets agent code call rlm_heartbeat.create/list/update/delete via host requests, handled by AgentSession when an rlmHeartbeatController is provided.
• Extends AgentSession follow-up queue with queueKey-based deduplication so repeated heartbeat triggers don't stack up.
• Adds a /heartbeat interactive slash command for setting, pausing, resuming, clearing, and viewing the session heartbeat.
• Risk: daemon startup now throws if agentDir is not configured; cron_cancel omits activeSessionId while other cron/heartbeat commands include it.

^{Macroscope summarized b4c99f5.}

---

Note

Medium Risk
Touches long-running daemon session lifecycle, automatic prompt injection, and persisted job state across restarts; incorrect scheduling or queue behavior could surprise users or duplicate work, though scope is localized to coding-agent daemon mode.

Overview
Adds daemon-backed scheduled prompts via a persisted cron-jobs.json store, an AgentCronScheduler, and CLI/protocol surfaces (daemon cron list|add|cancel, plus cron_* / heartbeat_* daemon commands). Due jobs wake or create the target session and inject prompts, with heartbeat-style jobs using per-job follow-up queue keys so busy sessions coalesce duplicate ticks instead of stacking identical follow-ups.

Introduces a user-owned /heartbeat slash command (set, pause, resume, clear, status) backed by the same cron machinery, with models limited to read-only get_heartbeat—no tool path to mutate the user heartbeat.

Adds the bundled rlm-heartbeat IPython skill (rlm_heartbeat.* host bridge) for session-scoped internal recurring checks, separate from /heartbeat, with multiple labeled jobs per session and controllers wired through main and subagent daemon runtimes. AgentSession gains optional followUpQueueKey coalescing and removeQueuedFollowUp for scheduler integration; session restore/rebind keeps jobs attached to the correct session file and active session id.

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