Before upgrade

• Open owncloud via the web interface as admin user
• Files | Apps (plus sign)
• Select "Enabled" on left side
• Make a note of all apps enabled
• Log out of owncloud

Upgrade

do upgrade using apt-get

Open command line

sudo su
su - www-data
cd owncloud
./occ upgrade
# Open a web browser to the Owncloud install. It will show to be in 
# maintenance mode and will return to the login screen when done
# go get a cup of coffee, it will take a good long while

• Open owncloud via the web interface as admin user
• Files | Apps (plus sign)
• Select "Not enabled" from left side
• Enable, at a minimum, Contacts, Calendar and Documents
• Enable any other apps you saw when you did the first step