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>

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