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If you are using EA2 and you want to replace with the 2.0 final release, do the following:
1. Configure the 2.0 final apex.war to point at your config folder:
java -jar apex.war configdir </path/to/config/folder>
where </path/to/config/folder> is the location of your config folder
2. Undeploy the EA2 apex.war in your application server
3. Deploy the 2.0.0 final apex.war in your application server
You can continue to configure multiple databases via the command line, nothing has changed in that regard. The SQL Developer option is for users who are more comfortable with using a graphical tool for administration.