The reason for this behaviour can be found in this thread: Subversive doesn't allow to commit "derived" resources. The folder used by the annotation processing and all contained resources automatically get the "derived" flag, which you can verify on their Properties->Resource page.
I'm in a similar situation as you wanting to commit generated files at least initially. There is a plugin that apparently makes it possible to override the behaviour of setting the "derived" flag, which I'm going to test now: AutoDeriv