Well, i just copied basically the whole folder of vanilla.winter into my mod but as a separate folder naming it "Winter". Then i put the normal maps in a different folder with all of my other models and changes naming it "Normal". I was planning on making models to add to the winter effect for guns and soldiers, but the game automatically uses vanilla models. I thought that maybe if I replace the soldier model xmls with my models it would use my models instead (using the same xml name). My mod wasn't fully updated to the newest version either, soo i had changed it and fixed for compatibility with 0.99.1 as well. But that still didn't work, I'm out of ideas sadly on how to fix this, and if you can't figure out a solution then its perfectly fine though.

I need some specifics about those folder locations to be able to help you.

Is it so that you copied vanilla.winter to media/overlays/your_mod/ named as Winter? That won't work, the game doesn't load such a folder as Winter there. You'd want to copy vanilla.winter at media/overlays/your_mod/packages/vanilla.winter. Then the game will use those files instead of media/packages/vanilla.winter when you enable the mod for a map that uses vanilla.winter, like map4 (Fridge Valley) or map12.

It also might be that you're not making an overlay mod at all but more like a complete content package which you pick maps from to load into, just like vanilla maps have it, so you'd have your files under media/packages/your_own_package.

I need more data

So as of right now my path for the folder is media/overlay/My Mod/packages/vanilla.winter/factions, models, textures, etc. I tried running the mod like this and it crashed immediately.