Did apt-get stop passing --force-overwrite to dpkg in the last few versions? I just did a dist-upgrade last night and for the first time got fatal errors for "xfree86-common: trying to overwrite file 'something/X11' which is also in package afterstep". I had to locate the debs in /var/cache/apt and dpkg -i --force-overwrite them myself. The other one that had a problem was emacs20.
I believe I can change /etc/apt/apt.conf to tell apt-get to always pass --force-overwrite to dpkg, but it isn't obvious that this is the right way to solve this problem. What should I do? Stuart.