I'm currently porting a WCF Service Project over to an Azure Role. Until now the library containing the service also hosted a Quartz.Net JobFactory for some lightweight background processing (perdiodically cleaning up stale email confirmation tokens). Do I have to move that code into a seperate worker role?
No you don't have to setup a separate worker role.
You simply have to start a background thread in your OnStart() Method of your Web Role. Give that thread a Timer object that executes your method after the given timespan.
Due to this you can avoid a new worker role.
class MyWorkerThread 
{
    private Timer timer { get; set; }
    public ManualResetEvent WaitHandle { get; private set; }
    private void DoWork(object state)
    {
        // Do something
    }
    public void Start()
    {
        // Execute the timer every 60 minutes
        WaitHandle = new ManualResetEvent(false);
        timer = new Timer(DoWork, null, TimeSpan.Zero, TimeSpan.FromMinutes(60));
        // Wait for the end 
        WaitHandle.WaitOne();
    }
}
class WebRole : RoleEntryPoint
{
    private MyWorkerThread workerThread;
    public void OnStart()
    {
        workerThread = new MyWorkerThread();
        Thread thread = new Thread(workerThread.Start);
        thread.Start();
    }
    public void OnEnd()
    {
        // End the thread
        workerThread.WaitHandle.Set();
    }
}
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