Perhaps it's a problem with git for Windows. I run in a, somehow, similar
situation using git for windows: in a branch, say branch-one, I have files
that didn't exists in branch-two. So changing from branch-one to branch-two
will result in all of these files that didn't exists in branch-two showing
up like untracked files.

Maybe you can try asking in the group for msysGit[1]

[1] = https://groups.google.com/forum/#!forum/msysgit

El abr 2, 2014 8:40 AM, "Stas Fedotov" <stas.fedo...@gmail.com> escribió:

> Hi!
>
> I have pretty much strange situation. Working on Windows machine and
> committing to Git Stash.
>
> In my global config I have core.autocrlf=true and there is .gitattributesin 
> repo with *
> text = auto
>
> Now here is what I do on clean, recently cloned repo:
>
> >git status #1on develop, no changes
>
> >git checkout -t origin/BRANCH-1 && git status #2
> Branch BRANCH-1 set up to track remote branch GPIII-96 from origin.
> Switched to a new branch 'BRANCH-1'
> modified: A.java
> modified: B.java
> modified: C.java
>
> >file A.java
> A.java: ASCII text, with CRLF line terminators
>
> >git rm --cached -r . && git reset --hard && git status
> # On branch BRANCH-1
> nothing to commit (working directory clean)
> **WTF??**
>
> >git checkout develop -f && git status
> modified: D.java
> **WTF???* **#remember on #1 it was OK*
>
> >git checkout BRANCH-1 -f && git status
> modified: A.java
> modified: B.java
> modified: C.java
> **WTF???**
>
>
> I am really not sure if it is connected to line-endings. I just have no
> idea how to check it.
>
> Any ideas on what's going on and how to fix that?
>
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