Each ebuild in the Portage tree used to come with its own digest file. When you emerged a package, this digest was used to verify that you had the same files the developer did. Until now.
A few days ago, all digest files were erased from the Portage tree as part of the final work to implement GLEP 44. This migrates that information to a single Manifest file per package instead of one digest for every ebuild of that package, which saves about 200MB of disk space in /usr/portage.