I don't know if this is by design or a bug, but alexpott and I noticed this while working on the Field API cmi conversion that has tests for create/change/delete.
If you copy a configuration file (that has changes of course) in the staging directory that also exists in your active directory without the manifest, it will be detected as an incoming change. It felt like a bug to us, so filing it whether this needs to be fixed or documented. I hope this isn't filed already though :)
Btw, nice job on the UI, it's becoming really cool playing around with CMI :)