The upgrade process can take a while, depending on the size of the projects portfolio. Do not refresh the web page after having launched the setup process as it will refresh automatically when the installation process is completed and the list of projects will appear. If you wish to monitor the process, you can look at the log file.
Using Atlassian Clover in version 1.10
The way code coverage tools are handled has slightly changed in version 1.10. The main difference is that Sonar now only authorizes one tool to be defined in general settings (as before you could use specify several) since you can override this information in project settings. Cobertura is selected by default. To use Clover, you have to set the property "General -> Code coverage plugin" to "clover".
For those who have migrated to 1.10
There was a slight issue on priority migration that is explained here.
Upgrade Maven plugin
Since release 1.8, you don't have to do anything to upgrade the Sonar Maven plugin. Command is :