Cron: persist manual run marker before unlock (#23993)

* Cron: persist manual run marker before unlock

* Cron tests: relax wakeMode now microtask wait after run lock persist

src/cron/service.issue-regressions.test.ts

@@ -507,6 +507,64 @@ describe("Cron issue regressions", () => {
     cron.stop();
   });
 
+  it("does not double-run a job when cron.run overlaps a due timer tick", async () => {
+    const store = await makeStorePath();
+    const runStarted = createDeferred<void>();
+    const runFinished = createDeferred<void>();
+    const runResolvers: Array<
+      (value: { status: "ok" | "error" | "skipped"; summary?: string; error?: string }) => void
+    > = [];
+    const runIsolatedAgentJob = vi.fn(async () => {
+      if (runIsolatedAgentJob.mock.calls.length === 1) {
+        runStarted.resolve();
+      }
+      return await new Promise<{ status: "ok" | "error" | "skipped"; summary?: string }>(
+        (resolve) => {
+          runResolvers.push(resolve);
+        },
+      );
+    });
+
+    let targetJobId = "";
+    const cron = await startCronForStore({
+      storePath: store.storePath,
+      runIsolatedAgentJob,
+      onEvent: (evt: CronEvent) => {
+        if (evt.jobId === targetJobId && evt.action === "finished") {
+          runFinished.resolve();
+        }
+      },
+    });
+
+    const dueAt = Date.now() + 100;
+    const job = await cron.add({
+      name: "manual-overlap-no-double-run",
+      enabled: true,
+      schedule: { kind: "at", at: new Date(dueAt).toISOString() },
+      sessionTarget: "isolated",
+      wakeMode: "next-heartbeat",
+      payload: { kind: "agentTurn", message: "overlap" },
+      delivery: { mode: "none" },
+    });
+    targetJobId = job.id;
+
+    const manualRun = cron.run(job.id, "force");
+    await runStarted.promise;
+    expect(runIsolatedAgentJob).toHaveBeenCalledTimes(1);
+
+    await vi.advanceTimersByTimeAsync(120);
+    await Promise.resolve();
+    expect(runIsolatedAgentJob).toHaveBeenCalledTimes(1);
+
+    runResolvers[0]?.({ status: "ok", summary: "done" });
+    await manualRun;
+    await runFinished.promise;
+    // Barrier for final persistence before cleanup.
+    await cron.list({ includeDisabled: true });
+
+    cron.stop();
+  });
+
   it("#13845: one-shot jobs with terminal statuses do not re-fire on restart", async () => {
     const store = await makeStorePath();
     const pastAt = Date.parse("2026-02-06T09:00:00.000Z");