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?