I have successfully added lenge to challenges mode in place of Dr thrax. dose anyone know where and how to edit ChallengeMode.wnd? Also some of the generals powers aren't selectable even though I am the right star level, any help on this?

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Open the .wnd in notepad, you should be able to edit it that way. At least, that is what I do.

As for the powers not being selectable, I am unsure because I have not tried adding the Boss General as a playable side. It is possible that the powers aren't linked to her; they may not have the correct sciences.

how could I link the correct sciences to her?

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Nevermind, it looks like the sciences and the generals powers are ok.