I figured out what my problem is. I had built compiz some months ago from source and installed it under /usr/local.
There was still some python stuff under there, and the new ccsm python script was importing the compizconfig module from under /usr/local, which is apparently in the python path first. When I built ccsm, it must have depended on the old protobuf stuff. So this is totally not a bug in the package dependencies. Sorry for the noise. By the way, I am really happy that compiz is back in Debian! I am a bit worried that I won't be able to use it, or that there will be not decent replacement for it, when it finally happens that I am forced to use wayland. Right now, I'm using compiz with xfce4. -- Thomas E. Vaughan
