It seems to me removeCombined
is the option you want. From the file that lists all options:
//If set to true, any files that were combined into a build bundle will be
//removed from the output folder.
removeCombined: false,
The false
value there shows the default.
By the way, it is really worth going through this file and looking at all the options because the page that introduces the optimizer is not by any means covering them all. Going through it again recently, I discovered an option that was added in the latest release of RequireJS.