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I just migrated my installation from owncloud 9 to nextcloud 9.0.50.
Only one thing is not working, the notes application simple shows me an empty list of notes. beside that, it is more like a new theme.

At the moment we only support manual migrations from ownCloud 8.2 and 9.0 to Nextcloud 9.

To do that please follow the usual upgrading steps:

* Delete everything from the ownCloud folder except data and config
* Download the Nextcloud 9 release from https://nextcloud.com/install/43
* Put the files into the folder where the ownCloud files where before
* Trigger the update either via OCC or via web.

I did the following steps.

#make a backup of your database
#log into your server and cd to the owncloud path
#
#assuming your installation is in the directory "cloud"
./occ maintenance:repair
cd ..
wget https://download.nextcloud.com/server/releases/nextcloud-9.0.50.zip
unzip nextcloud-9.0.50.zip
cp -rv cloud/config nextcloud/
cp -rv cloud/data nextcloud/
mv cloud owncloud
mv nextcloud cloud
cd cloud
./occ upgrade
./occ app:list
#enable the apps you want

Update from 2016-06-26
I created a small upgrade.sh script. Here it is.

#!/bin/bash                                                                                                             
####                                                                                                                    
# @author stev leibelt 
# @since 2016-06-26                                                                                                            
####                                                                                                                    
                                                                                                                        
#begin of runtime environment validation                                                                                
if [[ $# -lt 1 ]]; then                                                                                                 
    echo "invalid number of variables provided"                                                                         
    echo "upgrade.sh "                                                                         
    exit 1                                                                                                              
fi                                                                                                                      
                                                                                                                        
if [[ -d backup ]]; then                                                                                                
    echo "backup directory sill exists"                                                                                 
    exit 1                                                                                                              
fi                                                                                                                      
#end of runtime environment validation                                                                                  
                                                                                                                        
#begin of local runtime variables                                                                                       
LOCAL_CURRENT_DATE=$(date +'%Y-%m-%d')                                                                                  
LOCAL_URL_TO_THE_NEXT_VERSION="$1"                                                                                      
LOCAL_PUBLIC_BACKUP_PATH="public_$LOCAL_CURRENT_DATE"                                                                   
#end of local runtime variables                                                                                         
                                                                                                                        
#begin of downloading new version                                                                                       
wget $LOCAL_URL_TO_THE_NEXT_VERSION                                                                                     
unzip *.zip                                                                                                             
#end of downloading new version                                                                                         
                                                                                                                        
#begin of making backups                                                                                                
cd public                                                                                                               
tar --ignore-failed-read -zcf "public.$LOCAL_CURRENT_DATE.tar.gz" public                                                
./occ maintenance:singleuser --on                                                                                       
cd ../                                                                                                                  
mkdir backup                                                                                                            
cp -rv public/config backup/                                                                                            
cp -rv public/data backup/                                                                                              
mv public $LOCAL_PUBLIC_BACKUP_PATH                                                                                     
#end of making backups                                                                                                  
                                                                                                                        
#begin of upgrade                                                                                                       
mv nextcloud public                                                                                                     
cp -rv backup/config public                                                                                             
cp -rv backup/data public                                                                                               
cd public                                                                                                               
./occ upgrade                                                                                                           
./occ maintenance:singleuser --off                                                                                      
echo "enable the apps you need with ./occ app:enable "                                                            
./occ app:list                                                                                                          
#end of upgrade