I manage to got at least my system back!

Here are the steps to recover it (note that some steps might not be useful, but 
I'm unsure):
1. reboot in recovery mode
2. choose the root prompt with network

And then:
dpkg-reconfigure -a
dpkg --configure -a

At that point, I had a missing file /sbin/udevadm which prevents any further 
change to my packages system. So I launch another VM with just Ubuntu Live CD, 
I have installed SSH (using synaptics), and I did a scp on the Ubuntu Live VM 
to get that missing udevadm file. So something like:
scp [email protected]:/sbin/udevadm /sbin/

Then I did again:
dpkg --configure -a
It did work this time, and I went on:
apt-get -f install
apt-get --fix-missing install
apt-get update
apt-get upgrade
apt-get dist-upgrade
apt-get clean
apt-get autoremove
aptitude install ubuntu-desktop ubuntu-standard)
reboot

I have my system restored (or almost, the java, and a few other packages
where still missing). No data loss.

-- 
Computer Janitor wiped out most of my packages
https://bugs.launchpad.net/bugs/345939
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