The same thing happened to me.
I am in the middle of a project nearing a deadline and this is NOT ok. I like a lot of the features offered by GAE/GWT. But if Google thinks it's alright to break my development environment without asking, then they are not a safe technology provider.
I desperately hope someone from Google is reading this and taking action. I have the feeling they are about to lose a lot of developer support. I'm on the fence now and exploring other options. Too bad. These are such good tools.