I'm using following code to display help screen for the user
HelpFormatter formatter = new HelpFormatter();
HelpFormatter supports setting a different Comparator, see the javadoc.
Therefore it should be possible to add a new java.util.Comparator which knows about the intended order and set it for the HelpFormatter via
printHelp() should use the order that you provide.
If you cannot do that then the only option I see is to file an enhancement request with commons-cli.