apt-get automatically un installs necessary software

[theauditor]

My apt-get always shows the following message when I try to install or remove something.

Reading state information... Done
The following packages were automatically installed and are no longer required:
  baobab caribou caribou-antler dnsmasq-base empathy empathy-common fonts-cantarell gcalctool gdm3 gnome-backgrounds gnome-dictionary
  gnome-disk-utility gnome-font-viewer gnome-icon-theme-extras gnome-packagekit gnome-packagekit-data gnome-screenshot gnome-system-log gucharmap
  libavahi-gobject0 libavahi-ui-gtk3-0 libcaribou-gtk-module libcaribou-gtk3-module libchamplain-0.12-0 libchamplain-gtk-0.12-0 libgdict-1.0-6
  libgdict-common libgdu-gtk0 libgeocode-glib0 libjim0debian2 libmozjs22d libnl-route-3-200 libtelepathy-farstream2 libunique-3.0-0
  mobile-broadband-provider-info modemmanager nautilus-sendto-empathy network-manager network-manager-gnome sound-theme-freedesktop telepathy-gabble
  telepathy-logger telepathy-salut usb-modeswitch usb-modeswitch-data vino wpasupplicant xulrunner-22.0
Use 'apt-get autoremove' to remove them.

But note that most of the programs mentioned are required tools and are not unrequired dependencies as in normal case.

Then after few week when I try to install or uninstall something apt-get automatically starts removing these and all other programs that depend on it.
Leaving me with no Gnome, network-manager, wpasupplicant, grdm, and even apt-get itself. I then have to reinstall the entire os after backing up my home folder to get my system working again.

Last few times this happened when i tried to install the following

apt-get install gambas //2 months back
apt-get install ca-certificates //today

The following is the content of my sources.list

deb http://security.kali.org/kali-security kali/updates main contrib non-free
deb http://http.kali.org/kali	kali main contrib non-free

Please help me out as this is the 4th time I am reinstalling my entire OS due to this.

[blackMORE]

You're using Cinnamon or MATE? (or anything other than Default GNOME)? I can see caribou and baobab in the list.
Use

aptitude why-not gdm3

to find out the reason for autoremove suggestion. Work backwards.
Good luck.

[theauditor]

You're using Cinnamon or MATE? (or anything other than Default GNOME)? I can see caribou and baobab in the list.
Use

aptitude why-not gdm3

to find out the reason for autoremove suggestion. Work backwards.
Good luck.

It is a fresh install on which i just did "gnome-shell --replace " to get gnome3 shell.
Teh response for the command you gave was:

Unable to find a reason to remove gdm3.

[theauditor]

3 day bump

[theauditor]

bump anyone?

[0uroboros]

I'll second that bump. I had the same thing happen to me, but I use persistence, and I never really keep any data locally that I want permanently. So, I just deleted the extra stuff from that partition, and left only the persistence.conf file, rebooted, changed boot params appropriately, and went to work reconfiguring all my stuff all over again. I just get used to it.

Since no one is really reponding, I'll start at the low level. Have you checked your .iso? Your list of packages to be removed is identical to mine. I just don't ever use auto-remove, as a rule, because of things like this happening haha..

And I know it's a ridiculous question, but are you running auto-remove only because apt suggests it? After installing a couple things, I was no longer prompted like this..

[blackMORE]

It is a fresh install on which i just did "gnome-shell --replace " to get gnome3 shell.
Teh response for the command you gave was:

Unable to find a reason to remove gdm3.

I think I now understand what you tried to achieve. ... Get a proper GNOME instead of GNOME Fallback.

Determine current session

gsettings get org.gnome.desktop.session session-name

Get GNOME

dbus-launch gsettings set org.gnome.desktop.session session-name 'gnome'

Rollback:

dbus-launch gsettings set org.gnome.desktop.session session-name 'gnome-fallback'

I can not say how much changes were made in your system, but you could just do an apt-get install for the mentioned packages, and aptitude will stop bugging for removal.

apt-get install baobab caribou caribou-antler dnsmasq-base empathy empathy-common fonts-cantarell gcalctool gdm3 gnome-backgrounds gnome-dictionary gnome-disk-utility gnome-font-viewer gnome-icon-theme-extras gnome-packagekit gnome-packagekit-data gnome-screenshot gnome-system-log gucharmap libavahi-gobject0 libavahi-ui-gtk3-0 libcaribou-gtk-module libcaribou-gtk3-module libchamplain-0.12-0 libchamplain-gtk-0.12-0 libgdict-1.0-6 libgdict-common libgdu-gtk0 libgeocode-glib0 libjim0debian2 libmozjs22d libnl-route-3-200 libtelepathy-farstream2 libunique-3.0-0 mobile-broadband-provider-info modemmanager nautilus-sendto-empathy network-manager network-manager-gnome sound-theme-freedesktop telepathy-gabble telepathy-logger telepathy-salut usb-modeswitch usb-modeswitch-data vino wpasupplicant xulrunner-22.0

However, that's probably not the best way to go about it.