Goto bots folder right click and do an SVN check out. It will create the directory itself.
You have an extra folder layer is all. So the botbase is inside a folder with the same name prolly.
Yes, I have struggled how to adapt the layout that VS2013 creates (Project\Project) with what HB needs (Bot\Project). The way I found was to provide the link to Project\trunk\Project sub-directory on GitHub. You probably choose to ignore the link I've recommended and went for usual Project url. But if this works, it seems a proper way to go: no need to create a dir - will eliminate some errors. Just need to remove unneeded stuff. Thanks for the hint.