The commando tool bar, which can be enabled in the Console>General pane of the Global Options dialog box, has one button for each commando file. Clicking a button opens the commando window for that file.

By right-clicking on the buttons, you can hide or Customize each item.

If you select customize, the xml file will be opened into your current editor. If it's the first time you customized the button, and it came from inside the jar, then the file will be copied into your $HOME/.jedit/commando/ directory.

If you wish to un-hide buttons that are hidden, you can bring them back from Console's Toolbar Options pane.