Warning when certificates are left out of the managed git trust file

For Anthropic-managed git, the runner builds a certificate file. A runner is the machine that carries out Claude Code's work. Certificates are what git uses to decide which secure servers to trust. When Claude Code's deny list causes some certificates to be left out of that file, the runner now shows a warning. The warning gives how many were left out. It also explains that a git using this file will not trust those certificates for the managed git connection.