I'm not sure this is a bug or a feature, but as I'm adding the 50+ repo's I work with, the naming convention I'm working with has evolved as I've started to realise the extent of Automated builds possible with a DVCS.
Firstly, when I change some of the repositories names, Continua didn't then automatically change the old reference to the new reference within the existing project configurations I was using. Manually change was required. AKA. I had to find all the references to $Repository.xyz$ and change them.
Secondly cloning configurations and referencing a different "single" repository also requires you to step through every part of a configuration and ensure you are using the new repository. Again, it might be nice if Continua alerted you of the issue or, let the user decide if you want to automatically change the repository reference.