Atomic flag in git-fetch(1) doesn't cover pruning of refs

The --atomic flag in git-fetch(1) doesn't cover pruning of refs, so the guarantee that it's all-or-nothing doesn't hold. It also causes excessively many invocations of the reference-transaction hook in case many references are deleted (https://gitlab.com/gitlab-org/gitaly/-/issues/2436#note_834341201).