git's index broke and I was unable to restore it. While this is not git-annex' problem, it should still be possible to get my data in an un-annexed state.

    % git status
    fatal: index file smaller than expected
    % git annex unannex foo
    fatal: index file smaller than expected
    % git annex uninit
    fatal: index file smaller than expected
    uninit  
      pre-commit hook (/path/to/git-annex/.git/hooks/pre-commit) contents modified; not deleting. Edit it to remove call to git annex.
    ok
    %

Ttbomk, the softlinks and objects are enough to un-annex the files; side-stepping git's index if necessary.