Repair Cydia crash with apt-get for iPhone OS 4.1

iPhone 4.1 Cydia crashed on me because the Pwnagetool 4.1.2 jailbreak in expert mode installed outdated packages and missed some dependencies. To fix this I used the installed SSH connection to the iPhone to repair and update packages:

# apt-get update
# apt-get -f install
# apt-get dist-upgrade