I understand that for backwards compatibility the non-bare remotes use the old "mixed" case scheme. However, for new annexes, it'd make sense to be able to use the new one so the scheme matches in all remotes.

If this option existed then every clone of a repository would need to set it, or files would be hashed into the wrong location and would appear not visible. Sounds like a bug magnet to me; not attractive. --Joey

Actually, git-anex init -c annex.tune.objecthashlower=true does just this. So, done --Joey