JDK 1.6.x and Tomcat 6.0.x is required!
First of all; take a backup copy of your current installation, including the database!
Again, make sure that you have made a backup of your Tomcat webapp (all files) and the database!
Start to update your VisionFlow database by running the SQL script 'upgrade_from_v5.0_to_v5.1.sql' located in the directory: '\WEB-INF\internal_docs\installed version\db_scripts\v5.1\Upgrade from v5.0\'. Choose the directory that match your database, MS SQL Server or MySQL.
Unzip the vp_installed_v5.1_upgrade_from_v5.0.2-20090708.zip anywhere on your disk.
Remove all the files in the 'web-inf/lib' directory in your current installation.
Then you can copy your unzipped files from 3. into your VisionFlow webapp.
Merge the new VisionFlow.properties file in the 'web-inf/classes' dir with your old settings file to make sure your old settings is preserved and you also get any new settings that have been added.
You are done and can restart Tomcat again!