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The Vanilla game uses generic national flags for the campaign map because they represent nations and to deal with the issue that nations' battle flags changed over the period. As for me, I want to see the battle flag flying over Napoleon and his generals on the CAMPAIGN map: These are armies and cities under my military control, right?
So, I have created a mod that replaces the generic French flag flown over cities and armies with the infantry battle flag from the three periods covered by the game - the 1805, 1812, and 1815 patterns. You can choose the one you prefer, or just swap out the mod files manually when it's time: It's just a matter of swapping out the three files in the data folder.
I'll post here if there is any interest.