This may just be confusion in terminology, but the bot itself shouldn't be connecting to your repository. OSX Server does that. Before you can create a bot, you should've had to setup your repository in Server. When you do that, you get the opportunity to set username and password for accessing the repository.
It sounds like perhaps you have XCode configured to synch with your repository, but you must separately set up Server to access it as well. See the "XCode" tab in the Server app.