Git won't track empty directories (because at heart it only tracks files). Common advice is to add a '.gitkeep' file so the directory isn't empty and git will make the directory.

EVEN BETTER ADVICE: put a README in the directory explaining what the empty directory is for and what will eventually be there.

@nedbat But what do you do when all files from a folder are deleted in a certain commit. Leave a readme that this folder was once there for some kind of reason? Otherwise all people who once had pulled that commit end up with an empty folder that's not used for any thing...
@doekman @nedbat if you don't expect the folder to be used anymore, delete the folder as well. In other words, if you can't write a justification for that folders existence in the readme, it doesn't need to exist