Steps to reproduce: 1. Create some notes with the `git notes add` command. 2. Run `git notes` to list stored notes. 3. Run any of `git gc --prune=now` or `git pack-refs --all` commands. 4. Run `git notes` again and see that there are no more seen notes. The reason is that all commands like `git notes` or `git log --notes` expect to find notes head as unpacked ref in .git/refs/notes/commits. But the gc or the pack-refs command packs .git/refs/notes/commits ref into .git/packed-refs file. It's possible to restore the notes ref with a shell script like: ``` fix-notes-unpack-commits-ref(){ local hash path grep refs/notes/commits .git/packed-refs |\ while read hash path; do path=".git/$path" mkdir -p "$(dirname "$path")" echo -n "$hash" > "$path" done } ``` Or, fortunately, from another backup place: .git/logs/refs/notes/commits. The expected behavior is that `git notes` and `git log` should work also with notes ref stored in the .git/packed-refs file and also respect that the `git notes` command can store notes with a custom ref by using the `--ref` option. Yours sincerely, Andrew