- Something is out of sync. (Actually most likely it's just a spurious timestamp change.)
- Eclipse knows that it's out of sync.
- Eclipse launched into a lengthy operation assuming that everything it thinks about all the tens of thousands of files in the project will hold.
- It believed itself utterly helpless on finding that a file was out of sync.
(Yes, this problem occurs less often if I turn automatic refresh on. Bonus: Automatic refresh causes Eclipse to hold everything up for minutes at a time at unpredictable moments. Yay!)