I found that during indexing of a large organization folder, clicking the stop button does not abort the indexing.

if (Thread.interrupted()) {
    throw new InterruptedException();
}

needs to be inserted within loops. GitHubSCMNavigator.add is already doing this, so we need to determine why it is not working. Is something else clearing the interrupt status?

Would also be good to add a check to GitHubSCMSource.doRetrieve(SCMHeadObserver, ...), but much less important.