It appears none of the commenters understands how git reset works. Even if 
the problem is that Visual Studio messed up the git index, git reset should 
fix it. And if Visual Studio messed up the file (line endings or 
otherwise), the git reset --hard should revert it. This is certainly a bug 
in git for windows.

On Tuesday, February 23, 2016 at 12:34:32 PM UTC-6, Ben Page wrote:
>
> I have a couple repos that routinely believe there are local changes, when 
> there are none. The only solution seems to be to delete these files 
> and reacquire them from git.
>
> For example:
>
> >git status
> On branch master
> Your branch is behind 'origin/master' by 2 commits, and can be 
> fast-forwarded.
>   (use "git pull" to update your local branch)
> Changes not staged for commit:
>   (use "git add <file>..." to update what will be committed)
>   (use "git checkout -- <file>..." to discard changes in working directory)
>         modified: XXXXXXX
>         modified: YYYYYYY
> no changes added to commit (use "git add" and/or "git commit -a")
>
> >git --version
> git version 2.7.2.windows.1
>
> Reset doesn't work.
>
> >git reset --hard
> HEAD is now at cebdb13 Commit Message
>
> >git pull 
> Updating cebdb13..076de5e
> error: Your local changes to the following files would be overwritten by 
> merge:
>         XXXXXXX
>         YYYYYYY
> Please, commit your changes or stash them before you can merge.
> Aborting
>
> Checkout doesn't work
>
> >git checkout XXXXXXX
> >git checkout YYYYYYY
>
> >git pull
> Updating cebdb13..076de5e
> error: Your local changes to the following files would be overwritten by 
> merge:
>         XXXXXXX
> Please, commit your changes or stash them before you can merge.
> Aborting
>
> The only solution that I've found .
> >rm .git\index
> >rm XXXXXXX
> >rm YYYYYYY
> >git reset --hard
> >git pull
> Updating cebdb13..076de5e
> Fast-forward
> ...
>
> Can anyone help me understand why this is happening and how to avoid it?
>

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