Debian – apt wants to autoremove automatically installed recommended packages despite settings in apt.conf.d

APT maintains an indicator for each package, telling it whether the package is manually installed (installed because the user/administrator wanted it) or automatically installed (installed only because it's a dependency of some other package). That's what apt-get autoremove uses to determine what to remove: it removes packages that are marked as automatically installed, but that no currently installed package requires.

You need to mark the gnome package, or whatever Gnome package corresponds to the bits you want to keep, as manually installed. It's easiest to do this in an interactive tool with access to the automatically-installed setting:

• On the command line, call aptitude unmarkauto PACKAGENAME to mark PACKAGENAME as manually installed, or markauto to mark it as automatically installed.
• In Aptitude, move to the line corresponding to a package, then press m to mark it as manually installed, or M to mark it as automatically installed.
• In Synaptic, move to the line corresponding to a package, then toggle “Automatically installed” in the “Package” menu.

Note that (at least as of squeeze, I haven't checked wheezy) gnome-desktop-environment depends on all of the official Gnome components, including empathy. I suspect you had gnome-desktop-environment installed, and removing the empathy package had to remove it because of the dependency. If this is the case you should now reinstall gnome-desktop-environment. (If you don't remember, you can find a history of what APT-based package managers did in /var/log/apt.)

Instead of purging and installing empathy, you could have just done apt-get -t wheezy empathy to install the wheezy version.

apt-get autoremove or the aptitude equivalent removes all packages except the ones that have been installed explicitly (by selecting them in a package manager, or with apt-get install PACKAGENAME) and their dependencies. It doesn't know what packages might be important.

The manual/auto distinction can be very useful but you need to nudge it a bit. Declare key packages as explicitly installed, either with the apt-mark utility, or by running apt-get install (even if the packages is already installed), or by pressing m in the aptitude interface.

Debian and Ubuntu ship a number of metapackages that are there just to depend on certain categories of packages and which it's useful to install explicitly. That way, even if packages are reorganized on an upgrade, the dependencies will be managed automatically and you'll retain the functionality.

For example, in your case, you probably want something like

apt-get install xbase-clients
apt-mark manual ant libreoffice xorg

(and maybe a few more).