Hi I have just encountered the same problem with python-mode being removed when installing emacs-snapshot-gtk.
I solved the problem by building my own version of the package with emacsen added to the depends line in the control file. The new package works flawlessly. Please consider adding emacsen to depends so other users can benefit from this as well. I just checked jde and php-elisp and they too list emacsen in their depends. -- Regards, Martin Skøtt
