Windows 8.1 64-bit
git version 1.9.4.msysgit.0

I think I found a bug, but want to make sure before I actually say so.

Background: I've been trying to compile Qt, and after doing so decided I 
wanted to do it differently. The steps for this process involve fetching 
the various Qt modules with git and then calling `perl init-repository`, 
which changes the contents of the repo. (I'm not certain it actually 
changes any files, but it definitely adds several.)

`git status` showed lines resembling this:
modified:       <subfolder> (untracked content)

I found that these commands refused to properly restore me to a "pristine" 
state, matching my remote:
git checkout -- .
git checkout HEAD
git reset --hard
git clean -xdf

I also tried several variations on the above, but they didn't help and the 
listed versions seem to be recommended.

TortoiseGit ( reported a similar status, but was similarly 
ineffective at cleaning it up.

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