I\'m trying to rewrite my history in my git repository because I need to remove a file that contains restricted information.
This is what happens:
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This is mostly a guess, but the error may be caused by a bug that was fixed in git v1.7.7.1 (which was released after your original post). From the commit message:
Filter-branch already requires that we have a clean work tree before starting. However, it failed to refresh the index before checking, which means it could be wrong in the case of stat-dirtiness.