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See
<http://www.git.code-experiments.com/blog/2011/01/manage-large-files-with-git-annex-by-joey-hess.html>

If a local repo is cloned with "git clone orig/.git new", then git-annex in
new cannot see origin. 

the .git/config has "url=/.../orig/.git". Apparently git is ok with that
weird construction; probably it treats it as a bare git repo. But git-annex
just sees a directory w/o a .git subdir, and gives up.