From mboxrd@z Thu Jan  1 00:00:00 1970
From: Holger Hellmuth <hellmuth@ira.uka.de>
Subject: Re: The shared Git repo used by git-new-workdir
Date: Mon, 16 Jan 2012 20:15:22 +0100
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Cc: Git Users <git@vger.kernel.org>
To: Hilco Wijbenga <hilco.wijbenga@gmail.com>
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On 16.01.2012 19:57, Hilco Wijbenga wrote:
> In my working directory:
> hilco@centaur /mnt/lacie/workspaces/my-project-master
> my-project-master (master $ u=)$ git status
> # On branch master
> nothing to commit (working directory clean)
>
> In the shared repo:
> hilco@centaur ~/git-clones/my-project my-project (master +$ u=)$ git status
> # On branch master
> # Changes to be committed:
> #   (use "git reset HEAD<file>..." to unstage)
> #
> #       deleted:    .gitattributes
> #       modified:   .gitignore
> #       new file:   ...
> ... hundreds more ...

This is related to your using two repos with the same branch 
(irrespective of root repo or not).

There is nothing wrong with that per se, but if you add/commit/merge etc 
in one of those two, the working directory and index of the other repo 
doesn't get updated automatically. You would have to do "git reset 
--hard" in that repo to get it up-to-date

If you want to avoid this just don't check out the same branch in any 
two repos, root or not.