Could anyone explain what the function of the "Commands" and "Custom Tools" tabs are in the Customize dialog box or point me to the help file that does?
The commands tab is a list of commands that you can drag and drop onto Tool ars that you create in the first tab of the dialog - the toolbars when created in the first tab are empty and then you populate them with commands by drag and drop. If you use my custom ribbon it has a set of toolbars already defined and that shows how this works.
The Custom Tools I am not sure about without looking at it directly
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