Fix scheduled tasks disappearing after desktop app updates (#13627)

* Fix hub-managed schedules being wiped by cron reconciliation on hub restart

Co-authored-by: Saoud Rizwan <saoudrizwan@users.noreply.github.com>

* Require the virtual hub/schedules path when exempting specs from removal reconciliation

Co-authored-by: Saoud Rizwan <saoudrizwan@users.noreply.github.com>

* Treat recorded source mtime as proof a spec is file-backed, closing the hub/schedules spoof gap

Co-authored-by: Saoud Rizwan <saoudrizwan@users.noreply.github.com>

---------

Co-authored-by: Saoud Rizwan <saoudrizwan@users.noreply.github.com>

sdk/packages/core/src/cron/specs/cron-reconciler.test.ts

@@ -103,6 +103,59 @@ describe("CronReconciler", () => {
 		expect(all[0]?.removed).toBe(true);
 	});
 
+	it("does not remove hub-managed schedules with virtual source paths", async () => {
+		const created = store.createHubSchedule({
+			name: "Daily digest",
+			cronPattern: "0 9 * * *",
+			prompt: "Summarize the day",
+			workspaceRoot: "/ws",
+		});
+
+		// Simulates hub startup (e.g. after an app update) with no cron spec
+		// files on disk: DB-native hub schedules must survive reconciliation.
+		const summary = await reconciler.reconcileAll();
+		expect(summary.removed).toBe(0);
+
+		const schedule = requireValue(store.getSpec(created.specId));
+		expect(schedule.removed).toBe(false);
+		expect(schedule.enabled).toBe(true);
+		expect(store.listHubSchedules().map((s) => s.specId)).toContain(
+			created.specId,
+		);
+	});
+
+	it("still removes deleted file specs that spoof the hub-schedule source", async () => {
+		writeSpec(
+			"impostor.cron.md",
+			`---\nid: impostor\nworkspaceRoot: /ws\nschedule: "0 9 * * *"\nsource: hub-schedule\n---\nBody`,
+		);
+		await reconciler.reconcileAll();
+		const spec = requireValue(store.getSpecBySourcePath("impostor.cron.md"));
+		expect(spec.source).toBe("hub-schedule");
+
+		rmSync(join(cronDir, "impostor.cron.md"));
+		const summary = await reconciler.reconcileAll();
+		expect(summary.removed).toBe(1);
+		expect(requireValue(store.getSpec(spec.specId)).removed).toBe(true);
+	});
+
+	it("still removes deleted spoofing files inside a physical hub/schedules directory", async () => {
+		writeSpec(
+			"hub/schedules/nested-impostor.cron.md",
+			`---\nid: nested-impostor\nworkspaceRoot: /ws\nschedule: "0 9 * * *"\nsource: hub-schedule\n---\nBody`,
+		);
+		await reconciler.reconcileAll();
+		const spec = requireValue(
+			store.getSpecBySourcePath("hub/schedules/nested-impostor.cron.md"),
+		);
+		expect(spec.source).toBe("hub-schedule");
+
+		rmSync(join(cronDir, "hub/schedules/nested-impostor.cron.md"));
+		const summary = await reconciler.reconcileAll();
+		expect(summary.removed).toBe(1);
+		expect(requireValue(store.getSpec(spec.specId)).removed).toBe(true);
+	});
+
 	it("cancels queued runs when spec is removed", async () => {
 		writeSpec("cleanup.md", `---\nid: cleanup\nworkspaceRoot: /ws\n---\nBody`);
 		await reconciler.reconcileAll();

sdk/packages/core/src/cron/specs/cron-reconciler.ts

@@ -6,10 +6,11 @@ import {
 	resolveCronSpecsDir,
 } from "@cline/shared/storage";
 import { getNextCronTime } from "../schedule/scheduler";
-import type {
-	CronSpecRecord,
-	SqliteCronStore,
-	UpsertSpecResult,
+import {
+	type CronSpecRecord,
+	isHubManagedSpec,
+	type SqliteCronStore,
+	type UpsertSpecResult,
 } from "../store/sqlite-cron-store";
 import { type ParseCronSpecInput, parseCronSpecFile } from "./cron-spec-parser";
 
@@ -130,6 +131,10 @@ export class CronReconciler {
 			limit: 10_000,
 		});
 		for (const spec of existing) {
+			// Hub-managed schedules live only in cron.db with a virtual
+			// sourcePath (`hub/schedules/<id>.cron.md`) that never exists on
+			// disk — they must not be treated as deleted spec files.
+			if (isHubManagedSpec(spec)) continue;
 			if (!seenPaths.has(spec.sourcePath)) {
 				this.handleFileDeleted(spec);
 				summary.removed += 1;

sdk/packages/core/src/cron/store/sqlite-cron-store.ts

@@ -364,8 +364,28 @@ function filenameStemFromPath(sourcePath: string): string {
 		.replace(/\.md$/, "");
 }
 
+const HUB_SCHEDULE_SOURCE_PATH_PREFIX = "hub/schedules/";
+
 function hubScheduleSourcePath(scheduleId: string): string {
-	return `hub/schedules/${scheduleId}.cron.md`;
+	return `${HUB_SCHEDULE_SOURCE_PATH_PREFIX}${scheduleId}.cron.md`;
+}
+
+/**
+ * DB-native hub schedules (created via the schedule tools/UI) live only in
+ * cron.db under a virtual sourcePath that never exists on disk. File-backed
+ * specs can spoof `source: hub-schedule` in frontmatter — even inside a
+ * physical `hub/schedules/` directory — but reconciliation always records
+ * their source file's mtime, which DB-native rows never have. All three
+ * markers are required to identify a DB-native hub schedule.
+ */
+export function isHubManagedSpec(
+	spec: Pick<CronSpecRecord, "source" | "sourcePath" | "sourceMtimeMs">,
+): boolean {
+	return (
+		spec.source === "hub-schedule" &&
+		spec.sourcePath.startsWith(HUB_SCHEDULE_SOURCE_PATH_PREFIX) &&
+		spec.sourceMtimeMs === undefined
+	);
 }
 
 function hubScheduleMetadata(