As this was discussed in the ticket as well. I am adding reply also in here.
All actions that are possible to perform on the API are in CMS.ContinuousIntegration namespace. You could use FileSystemRepositoryManager class and methods Store(), StoreAll(), RestoreAll() to work with the repository.
Since CI objects are part of a repository under some source control, you can also use the some console application to run the ContinuousIntegration.exe and do this without Kentico at all.