git: Update to v2.31.1

Git v2.31.1 has been released on October 12th with a big range of fixes. Most relevant to us, it also contains fixes for git-update-ref(1) to properly flush output when having a conversation with --stdin, which we're currently carrying a custom patch for.

Bump our Git version to v2.31.1 and drop the custom patch. Furthermore, adjust FlushesUpdaterefStatus() to reflect that v2.31.1 now support flushing.