I think something's wrong with the apps the ebuild maintainers use to publish ebuilds to the rsync mirrors. Manifest files are missing from whole categories like gnome-base and net-mail, while others like gnome-apps and gnome-libs are completely devoid of files. Nothing in them but empty directories. I've tried several rsync mirrors from different countries, and the results are the same.
manifests are in the process of being implemented. A manifest is added to a package only when said package is updated, such as for a version bump or bugfix. As such, not all packages will contain full manifests yet. So, what you're reporting is expected behavior. Downgrading severity. Marking as invalid.
