As you can see, I'm running a pretty recent build of git-annex (ac799c3f363e0008b23e9c174e6fedc35e6fa92a),

    $ git annex version
    git-annex version: 3.20120630
    local repository version: 3
    default repository version: 3
    supported repository versions: 3
    upgrade supported from repository versions: 0 1 2

We have a file here which isn't currently available yet isn't
currently available (the link is shown in red),

    $ ls -l plot.py
    lrwxrwxrwx 1 ben ben 77 Jul  6 14:01 plot.py -> ../.git/annex/objects/WORM:1301941019:720:plot.py/WORM:1301941019:720:plot.py
    $ 

Yet git-annex should be able to tell us where it is,

    $ git-annex whereis plot.py
    $ 

Hmm, well that's strange. What's happening here,

    $ git-annex whereis plot.py -d
    git ["--git-dir=/home/ben/lori/analysis/data/.git","--work-tree=/home/ben/lori/analysis/data","show-ref","git-annex"]
    git ["--git-dir=/home/ben/lori/analysis/data/.git","--work-tree=/home/ben/lori/analysis/data","show-ref","--hash","refs/heads/git-annex"]
    git ["--git-dir=/home/ben/lori/analysis/data/.git","--work-tree=/home/ben/lori/analysis/data","log","refs/heads/git-annex..d5582e05f41011b571a17003934fe9e40859e4be","--oneline","-n1"]
    git ["--git-dir=/home/ben/lori/analysis/data/.git","--work-tree=/home/ben/lori/analysis/data","cat-file","--batch"]
    git ["--git-dir=/home/ben/lori/analysis/data/.git","--work-tree=/home/ben/lori/analysis/data","ls-files","--cached","-z","--","plot.py"]
    $ 

Alright, well maybe `git-annex get` will work,

    $ git annex get plot.py -d
    git ["--git-dir=/home/ben/lori/analysis/data/.git","--work-tree=/home/ben/lori/analysis/data","ls-files","--cached","-z","--","plot.py"]
    $ ls -l plot.py
    lrwxrwxrwx 1 ben ben 77 Jul  6 14:01 plot.py -> ../.git/annex/objects/WORM:1301941019:720:plot.py/WORM:1301941019:720:plot.py

Nope, the link is still shown in red.

Alright, what about `git-annex copy`?

    $ git annex copy plot.py --from=goldnerlab --to=here -d 
    git ["--git-dir=/home/ben/lori/analysis/data/.git","--work-tree=/home/ben/lori/analysis/data","show-ref","git-annex"]
    git ["--git-dir=/home/ben/lori/analysis/data/.git","--work-tree=/home/ben/lori/analysis/data","show-ref","--hash","refs/heads/git-annex"]
    git ["--git-dir=/home/ben/lori/analysis/data/.git","--work-tree=/home/ben/lori/analysis/data","log","refs/heads/git-annex..d5582e05f41011b571a17003934fe9e40859e4be","--oneline","-n1"]
    git ["--git-dir=/home/ben/lori/analysis/data/.git","--work-tree=/home/ben/lori/analysis/data","cat-file","--batch"]
    git ["--git-dir=/home/ben/lori/analysis/data/.git","--work-tree=/home/ben/lori/analysis/data","ls-files","--cached","-z","--","plot.py"]
    $ ls -l plot.py
    lrwxrwxrwx 1 ben ben 77 Jul  6 14:01 plot.py -> ../.git/annex/objects/WORM:1301941019:720:plot.py/WORM:1301941019:720:plot.py

Still red.

Alright, what if I just try to get a non-existent file?

    $ git annex get adsflkah -d
    git ["--git-dir=/home/ben/lori/analysis/data/.git","--work-tree=/home/ben/lori/analysis/data","ls-files","--cached","-z","--","adsflkah"]
    $

Alright, it didn't fail with an error, that's very strange. What is going on here?