When I create a new repository it doesn't download all directories/files, why does it not work?

[Tim Crall]

Can you describe more specifically (perhaps with screenshots) the steps you're following?

If you create a new repository on Bitbucket, it should be initially empty.  Then you can clone it, add files, commit, and push back to the server.

[Gareth Jones]

Are there any files in the folders? Git sort of ignores empty folders, it's tracking files so it there aren't any files the folder doesn't exist.