fix: sub-agent hang/crash stranding runs mid-phase with no save

A stalled sub-agent (provider stream never settling after the final tool
call, or a throwing session-event listener recursing through the SDK's
run-failure path to stack overflow) left the phase stuck in_progress with
no state save, no error, and no completion message — observed twice in
freno-dev, both times after comments wrote findings.md.

- agent-runner: 60-min settle watchdog on every agent phase
  (PYGIENIUM_AGENT_TIMEOUT_MS, env-tunable); timeout disposes the session
  and fails the phase loudly with a /pygienium-resume hint instead of
  hanging the check-runner's await forever.
- agent-runner: applySessionEvent — the session.subscribe listener can no
  longer throw into the SDK event pipeline (guards for partial/malformed
  events, optional-chained message_update, throwing chat forwarder).
- comments: scan no longer regenerates the full report as its final
  message (findings.md is the source of truth); fix phase reads
  findings.md with embedded fallback.
- check-runner: failing state-save inside the catch path can't double-
  fault or escape as an unhandled rejection; completion posting is
  best-effort.
- tests: watchdog timeout test, comments task-text regression tests,
  applySessionEvent malformed-shape unit tests. 146 pass, tsc clean.
- README: document PYGIENIUM_AGENT_TIMEOUT_MS.

tests/check-runner.test.ts

@@ -20,6 +20,8 @@ import {
 	setAgentRunner,
 	resetAgentRunner,
 	fakeAgentRunner,
+	AGENT_TIMEOUT_ENV,
+	type AgentRunResult,
 } from "../src/agent-runner.js";
 import { handleCheckCommand, type PygieniumCtx } from "../src/commands.js";
 import { loadRunState, runStatePath } from "../src/run-state.js";
@@ -128,4 +130,29 @@ describe("check-runner integration", () => {
 		expect(state?.checks.gated.status).toBe("skipped");
 		expect(state?.checks.gated.error).toBe("no source files matched");
 	});
+
+	it("fails the check loudly when the agent never settles", async () => {
+		// Models the silent hang: the sub-agent session never resolves after
+		// its last tool call (stalled provider stream / hung retry), leaving
+		// the run stuck mid-phase with no state save and no completion. The
+		// watchdog must abort the phase with a visible error instead.
+		setAgentRunner(() => new Promise<AgentRunResult>(() => {}));
+		const prev = process.env[AGENT_TIMEOUT_ENV];
+		process.env[AGENT_TIMEOUT_ENV] = "50";
+		try {
+			await handleCheckCommand(smokeCheck(), "", stubCtx(cwd));
+		} finally {
+			if (prev === undefined) delete process.env[AGENT_TIMEOUT_ENV];
+			else process.env[AGENT_TIMEOUT_ENV] = prev;
+		}
+
+		const state = await loadRunState(cwd);
+		expect(state?.checks.smoke.status).toBe("failed");
+		expect(state?.checks.smoke.error).toContain("did not settle within");
+		expect(state?.checks.smoke.error).toContain("/pygienium-resume");
+		expect(
+			state?.checks.smoke.phases.find((p) => p.id === "analysis")?.status,
+		).toBe("failed");
+		expect(state?.status).toBe("failed");
+	});
 });