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I'm using emacs on Windows and this is long bothered me. All other apps correctly ignore all listed in global .gitignore, but in emacs they are untracked/unregistered and pollute the status window.

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    I just tested both vc-dir and magit. I had an unregistered file which was shown as such in both interfaces, then I added it to ~/.config/git/ignore, and both vc-dir and magit saw it as "ignored". IOW : I can't reproduce on emacs (from git master branch) and the latest magit release (I'm on GNU/Linux).
    – YoungFrog
    Jul 21, 2015 at 7:56

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Reset to default
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It turned out Emacs's HOME and Git's were different. I've added the HOME environment variable and moved my .emacs there. All works fine now. Thanks @YoungFrog, you made me think about my HOME.

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