[[!comment format=mdwn
 username="joey"
 subject="""comment 1"""
 date="2016-04-20T18:14:25Z"
 content="""
So the directory structure got lower cased when you copied it from OSX to
linux. OSX remembered a lower-case name for the J4 directory, for example,
and propigated that over to linux.

Unfortunately, git-annex is stuck using mixed case hash directories for
backwards compatability reasons. Changing to all lower-case hash
directories would need every git-annex repo to be converted; would
invalidate all old tags and branches and history in the repos, etc.
This is discussed in [[design/new_repo_versions]].

It's actually possible to make brand-new git-annex repos use all lower case
hash directories today, by setting `git config annex.tune.objecthashlower true`
before you run `git annex init` for the first time. 

If you know you will need to move a repository between case-insensative and
case-sensative filesystems, you could use that configuration. But that
would be very forward looking, and instead users are just going to stumble
over the mixed case directories from time to time.

What I'd recommend you do is, move the repository back to OSX, and then
make a clone of it on the linux system, and use `git annex move --all
--from origin` to move all the annexed file contents over from OSX to
linux. This method avoids the problem entirely.
"""]]