I just released Netatalk 2.0.3-2. This version solved the conflict with yudit by renaming /usr/bin/uniconv to /usr/sbin/netatalk-uniconv. As this is a tool that is only required very occasionally (i.e. when updating a volume from one character set to unicode, which hopefully you will only have to do once per volume), this change should be fairly unobstrusive.
Resolving the conflict with bigloo is more bothersome. Bigloo also contains a binary called afile, just like Netatalk. But since this is a tool that is possibly used regularily by some users and may even be used in scripts, I fear that simply renaming it may break things. I think I will just try to rename afile (and a few other similar commands) to apple_file, add a note to NEWS.Debian, and upload this to unstable. If too many users complain, I will probably use a transitional strategy: Rename the tools, add the note to README.Debian, but leave symlinks hanging around until after the release with etch. This would mean that the conflict with bigloo can’t be resolved until then.
Other opinions or suggestions on that matter are welcome.