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+git-annex commands that take a file path as argument but really operate on the key corresponding to the file's contents, when given an unlocked file that has been modified, will operate on the original key, not the key corresponding to the file's current contents.  For example, [[`git-annex-whereis`|git-annex-whereis]] can show that there are several copies of the contents, even though there is only one (and only in the working copy).