All menus disappeared after apt-get upgrade

[Shar]

Dear Sirs,
I installed fresh Linux Kali. Below are details when perfomed cat /etc/*-release

DISTRIB_ID=Kali
DISTRIB_RELEASE=kali-rolling
DISTRIB_CODENAME=kali-rolling
DISTRIB_DESCRIPTION="Kali GNU/Linux Rolling"
PRETTY_NAME="Kali GNU/Linux Rolling"
NAME="Kali GNU/Linux"
ID=kali
VERSION="2016.1"
VERSION_ID="2016.1"
ID_LIKE=debian
ANSI_COLOR="1;31"
HOME_URL="http://www.kali.org/"
SUPPORT_URL="http://forums.kali.org/"
BUG_REPORT_URL="http://bugs.kali.org/"

My sources.list content is (The Kali Rolling Repository)

deb http://http.kali.org/kali kali-rolling main contrib non-free
# For source package access, uncomment the following line
deb-src http://http.kali.org/kali kali-rolling main contrib non-free

I have done the following
apt-get update
Then
apt-get upgrade

I waited around 35-50 minutes.

When finished everything, the system rebooted itself.
However
(1) I cannot see any menu item (All of them disappeared)
(2) I cannot open anything (for example Terrminal, Firefox, etc). When I try to open for example Terminal or Firefox, this causes the system to reboot it self.

Please help. I have now installed fresh Kali Linux again. I want to perfrom apt-get update then apt-get upgrade. But I also wich not to see the problem again.

Your help is very much appreciated.
I am stacked. I cannot go forward.

[_defalt]

deb http://http.kali.org/kali kali-rolling main contrib non-free
# For source package access, uncomment the following line
deb-src http://http.kali.org/kali kali-rolling main contrib non-free

Carefully read this bold line and try to understand what it says and what you should have done before crashing your system with another active repository.

[Shar]

Carefully read this bold line and try to understand what it says and what you should have done before crashing your system with another active repository.

Thank you very much for your kind help and quick reply.

These are what I copied from repository
deb http://http.kali.org/kali kali-rolling main contrib non-free
# For source package access, uncomment the following line
# deb-src http://http.kali.org/kali kali-rolling main contrib non-free

Is that means I should not have removed the comment before debs-rrc. Did the system crashed because I removed the comment?

Now I have reinstalled the Kali Linux. I want to perform apt-get update then apt-get upgrade. Can I use the repository code as copied
deb http://http.kali.org/kali kali-rolling main contrib non-free
# For source package access, uncomment the following line
# deb-src http://http.kali.org/kali kali-rolling main contrib non-free

Without removing the hash befoe deb-src.

Thank you

[_defalt]

In your first post there was no hash # before deb-src which is incorrect. Developers itself are telling that to uncomment the second entry by putting hash before it. If your original repositories before crashing were these:
deb http://http.kali.org/kali kali-rolling main contrib non-free
# For source package access, uncomment the following line
# deb-src http://http.kali.org/kali kali-rolling main contrib non-free
Then it was correct. Most of the people forget to uncomment the second one.

If the problem is caused while keeping above entries as shown then your problem with menu was not due to incorrect repositories.

[_defalt]

Is that means I should not have removed the comment before deb-src. Did the system crashed because I removed the comment?

Yes you shouldn't have removed the hash from the second entry. The possible reason is that your kali is crashed by keeping wrong entries. Developers always warn that your OS may go in unusable state if repositories are incorrect.

[Shar]

Thank you for your reply.
I have followed your advice
1) Updated the sources.list as
deb http://http.kali.org/kali kali-rolling main contrib non-free
# For source package access, uncomment the following line
# deb-src http://http.kali.org/kali kali-rolling main contrib non-free

2) I have updated using
apt-get update
3) I have upgraded using
apt-get upgrade

Still, I am getting the same problem. All the icons disappeared and I cannot open any application for example the browser, the Terminal. When I try to open it the System reboots itself.

Please help. All that I want to solve is
E: Unable to locate package tomcat7
when I want to install tomcat7 using
apt-get install tomcat7

Your help is very much appreciated