Methods that Clear the Thread.interrupt() flag

Part of the problem has been that I do not know every method call out there that clears the interrupt flag.

It is important to clarify that the following methods clear the interrupt flag by just calling them:

Thread.interrupted()
Thread.isInterrupted(true) -- added to your list

For this reason Thread.currentThread().isInterrupted() should always be used instead.

The following methods will clear the interrupted flag by immediately throwing InterruptedException either if they were called and then the thread was interrupted or if the thread was already interrupted and then they were called (see junit code below). So it is not the method that clears the flag, throwing the exception does.

Your initial list:

Thread.interrupted()
Thread.sleep(long)
Thread.join()
Thread.join(long)
Object.wait()
Object.wait(long)

Added to your list:

Thread.sleep(long, int)
Thread.join(int, long)
Thread.isInterrupted(true)
Object.wait(int, long)
BlockingQueue.put(...)
BlockingQueue.offer(...)
BlockingQueue.take(...)
BlockingQueue.poll(...)
Future.get(...)
Process.waitFor()
ExecutorService.invokeAll(...)
ExecutorService.invokeAny(...)
ExecutorService.awaitTermination(...)
CompletionService.poll(...)
CompletionService.take(...)
CountDownLatch.await(...)
CyclicBarrier.await(...)
Semaphore.acquire(...)
Semaphore.tryAcquire(...)
Lock.lockInteruptibly()
Lock.tryLock(...)

Please note that the proper pattern with any code that catches InterruptedException is to immediately re-interrupt the thread. We do this in case others are relying on the thread.isInterrupted() method:

try {
    ...
} catch (InterruptedException e) {
    // immediately re-interrupt the thread
    Thread.currentThread().interrupt();
    // log the exception or [likely] quit the thread
}

JUnit code that demonstrates some of this:

assertFalse(Thread.currentThread().isInterrupted());
// you can do this from another thread by saying: someThread.interrupt();
Thread.currentThread().interrupt();
// this method does _not_ clear the interrupt flag
assertTrue(Thread.currentThread().isInterrupted());
// but this one _does_ and should probably not be used
assertTrue(Thread.interrupted());
assertFalse(Thread.currentThread().isInterrupted());
Thread.currentThread().interrupt();
assertTrue(Thread.currentThread().isInterrupted());
try {
    // this throws immediately because the thread is _already_ interrupted
    Thread.sleep(1);
    fail("will never get here");
} catch (InterruptedException e) {
    // and when the InterruptedException is throw, it clears the interrupt
    assertFalse(Thread.currentThread().isInterrupted());
    // we should re-interrupt the thread so other code can use interrupt status
    Thread.currentThread().interrupt();
}
assertTrue(Thread.currentThread().isInterrupted());

Common convention is the following: any method that throws InterruptedException (+ Thread.interrupted()) clears the interrupt flag.

So, in order to make your threads interruptable you need to find all places where InterruptedException gets caught without retrowing it or restoring the interrupt flag. Since InterruptedException is a checked exception it's not hard to do.