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I would expect the "Add" button to ask me for a name for the new rule file, and then add it to the list of commands (in the selected category), and perhaps immediately open it in the editor. Instead it opens a filechooser (do you need to have an existing rule file somewhere?), which is not consistent with the behavior of any similar manager dialog I can think of. Should perhaps also be called "New". Or if there is a reason to add rules that are saved on disk somewhere, at least "Add" should open a simple dialog with radio buttons: (*) Create new rule file Name: [____________________________] ( ) Add existing rule file Location: [________________] [Browse...]
Please review the <a href="http://jackpot.netbeans.org/docs/jackpot-uispec.html">Jackpot UI Spec</a>, which proposes a replacement for the Command Manager which should address your concerns.
The new Refactoring Manager works as you describe; click the New Query... button to try (after it is pushed to update center, of course).