I am tinkering around with some textures and noticed that there are actually two folders for the minecraft textures, unity and minecraft. Looks like unity contains alternative textures like the 3 obsidian ones and minecraft really just holds the vanilla ones. The olny thing that I find strange is that the carrot textures are under the unity folder too.
So how are files organized within the asset folder? What makes files go intio ùnity instead of minecraft?

The unity directory is for textures that don't overwrite anything existing. There are still remaining files in other directories that ideally need to be moved to unity, it just hasn't been done yet.

The unity directory is for CTM and randomized textures.

Thanks for the answers!