I know the problem exists both on PC and Mac.  My team can replicated on 
two different PC running Windows 7 and 10.

For Mac, I am using El Capitan, the git version I am using is version 
2.8.2.  I am seeing that.    I have also confirmed with a separate group 
that worked on LFS, they have to do something special for this special case 
because they also use git filters.  We use similar methodology for the team 
that implements LFS to create our filters.  Maybe, you can help us to 
understand what we did wrong with the way we configure the filter.   For 
below example, 'irongit' is the filter program we use.

Here is what I did:
% git add .
% git commit -m "checking all things in"
% git push

All the above was executed successfully.  Then, I do:
% git diff
<<<< nothing shows up
% git diff --name status
M       0-bytefile1
M       0-bytefile2
M       0-bytefile3
<<<<<< above only list zero byte file in my git repository. 

This is the modified ./git/config for the filters.
        repositoryformatversion = 0
        filemode = true
        bare = false
        logallrefupdates = true
        ignorecase = true
        precomposeunicode = true
[remote "origin"]
        url = ssh://git@xxxx.yyyyzzzz:1234/myproject/repo.git
        fetch = +refs/heads/*:refs/remotes/origin/*
[branch "master"]
        remote = origin
        merge = refs/heads/master
[filter "atcipher"]
        smudge = irongit decrypt %f
        clean = irongit encrypt %f
        required = true
[diff "atcipher"]
        textconv = cat
[merge "atcipher"]
        name = irongit merge driver
        driver = irongit merge %O %A %B %P

On Thursday, May 5, 2016 at 8:28:43 AM UTC-7, Jack Poon wrote:
> Hi,
> We are working on an add-on over git using git filters, and testing other 
> tools that encapsulate Git.
> For some reason, git reports that there is difference for any zero-byte 
> when git filters are used.
> Is this a feature or bug?  What's the suggested workaround?
> Best regards,
> Jack

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