These interactions with grafts, replace-objects, and shallow clones are one reason 2.18 does not create and manage this file automatically. The commit-graph file works by representing the commit relationships in a new file, and if that file exists, we treat that as the truth. The commit grafts, replace-objects, and shallow clones use another set of special files to track commits whose parents have been modified in special ways. If you would like to see our progress on integrating these features together, please see this thread on the Git mailing list: https://public-inbox.org/git/20180531174024.124488-1-dstolee...