I'm having similar issues, using BT5-32gnome.
I did a fresh install of BT5 this morning, then
# apt-get update
# apt-get upgrade
# apt-get dist-upgrade
After doing so, all of my msf* symbolic links are broken.
i.e. /usr/local/bin/msfupdate or /usr/local/bin/msfconsole
The directory /opt/framework3/app/ is gone.
I've searched for msfconsole to see if it was installed elsewhere and this is all that shows up from my search
# find / -name msfconsole
/usr/local/bin/msfconsole (broken sym link -> /opt/framework3/app/msfconsole)
Any assistance would be greatly appreciated.