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From the Connections view, right-click on any connection. You will see Add to Folder -> New Folder -> Folder Name. Once you have created the folder and added the first connection, just highlight multiple other connections that belong in the same folder, right-click, Add to Folder -> <select target folder name from the list>.
Other areas in the tool, like the Worksheet ConnectionSelectorUI widget's (upper right corner) drop-down list, will still display all the connections in a single, flat listing. An enhancement request has already been logged.
SQL Developer Team