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When I run `git annex unused` from my repository's root it shows everything ok:

    ~/annex$ git annex unused
    unused  (checking for unused data...) ok

But... When I run it from a subdirectory, it shows a lot:

    ~/annex/Software$ git annex unused
    unused  (checking for unused data...) 
      Some annexed data is no longer pointed to by any files in the repository:
        NUMBER  KEY
        1       SHA1:########################################
    ...
        921     SHA1:########################################
      (To see where data was previously used, try: git log --stat -S'KEY')
      (To remove unwanted data: git-annex dropunused NUMBER)
      ok

Is this a bug or by design? By removing these "unused" files with `dropunused` I've just lost the only copy of 160 files.

I am using git-annex version 836e71297b8e3b5bd6f89f7eb1198f59af985b0b