After upgrading to bookworm I also got bitten by this issue. Otherwise the upgrade went smoothly.
I noted that at least for some of the superfluous files, the cruft tool (from package cruft-ng) reports that a file belongs to the package emacs, while it does not according to dpkg -L or dpkg -S: # cruft /usr/share/emacs/site-lisp/elpa/org-9.4/org.elc emacs # dpkg -L emacs /. /usr /usr/share /usr/share/doc /usr/share/doc/emacs /usr/share/doc/emacs/changelog.Debian.gz /usr/share/doc/emacs/copyright (I do not know who’s the culprit here, just noting in case other people who read this have a better understanding.) ---------------------------------------------------------------- Since I was not sure what’s going on and I needed a properly working Emacs installation quickly, I simply uninstalled all packages named by “dpkg -S /usr/share/emacs”, removed /usr/share/emacs (which contained a lot of cruft at that point), and reinstalled the previously removed packages again.
