You could potentially add a new field called "subdirectory to monitor", and have its default value be "branches". That way existing users could migrate to the new version, while getting the previous behavior, and new users can change this to get the new behavior.
You would also need to change other places that mention "monitored branches" and similar terminology, to "monitored subdirectories" though.
Even better, you can add another field called "monitor subdirectories" with a default value of true. In my case, I don't really want to monitor subdirectories, just one directory.
I'll probably play around with the plugin code to see what I can do.
Thanks