From mboxrd@z Thu Jan  1 00:00:00 1970
From: Mark Levedahl <mlevedahl@gmail.com>
Subject: Re: regression in git-gui since 2c5c66b... Merge branch 'jp/get-ref-dir-unsorted
Date: Sun, 16 Oct 2011 21:38:33 -0400
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To: Junio C Hamano <gitster@pobox.com>
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On 10/16/2011 08:35 PM, Junio C Hamano wrote:
> Mark Levedahl<mlevedahl@gmail.com>  writes:
>
>> I have a project organized as a number of nested git modules (not
>> using git-submodule), and frequently use git-new-workdir to create the
>> nested modules.
>>
>> Since the above merge-commit, git-gui is confused by this arrangement
>> and reports every file in every nested module as being an untracked
>> file in the top-level (super) project.
> Could you come up with a simple reproduction recipe that prepares a
> superproject that has no file of its own, a submodule with a single file
> tracked, and attaches another workdir? If running git-gui in the resulting
> directory makes it misbehave, we could then isolate what git command that
> is invoked by git-gui has changed its behaviour.
>
> Thanks.
>

The following shows the problem for me:

#!/bin/bash
mkdir super sub
cd sub
git init
touch a
git add a
git commit -m 'file' a
git pack-refs --all
cd ../super
git init
git new-workdir ../sub sub
git-gui


git-gui shows "sub/a" in the list of Unstaged Changes. Note that the 
"git pack-refs" call is needed to get the failure.

Mark