As the maker of a mod manager that has to parse versions from mod_info.json, I hate you.
As a player of the game, I love you, these are wonderful.
My only bit of feedback (and I'll probably just make a personal edit since you were kind enough to provide the files) is that the Hegemony losing their orange makes their flag much harder to recognize at a glance when it's tiny.
When flags are small, their color is the primary way to discern them.
Oh, I'm sorry I made you sad. I am not really a technical person, and I'm not all that great with code. If there is something I can do better to help you out with your management, I am open to feedback and guidance.
As for the color, yeah, I get what you mean, although I never liked the fact that the faction is orange in the first place due to how close it is to the yellow of the Persan Legion. In my opinion they could have been a dark green or something, but that's just my take on it. Of course, I do not mind if you want to fork my work and put your own details in the designs. I have to admit that it was the first flag I made so I plaid with a lot of elements before I settled on this version and I really didn't find a "way" to make the orange color stick to it, in order to satisfy my mental itches.