title: git cannot add or checkout some files
body: <p>I use git to clone this repo, <a href="https://git.kernel.org/pub/scm/linux/kernel/git/torvalds/linux.git" rel="nofollow noreferrer">https://git.kernel.org/pub/scm/linux/kernel/git/torvalds/linux.git</a></p>
  
  <p>After done, I find some files are changed, shown by <code>git status</code>.</p>
  
  <pre><code> M include/uapi/linux/netfilter/xt_CONNMARK.h
   M include/uapi/linux/netfilter/xt_DSCP.h
   M include/uapi/linux/netfilter/xt_MARK.h
   M include/uapi/linux/netfilter/xt_RATEEST.h
   M include/uapi/linux/netfilter/xt_TCPMSS.h
   M include/uapi/linux/netfilter_ipv4/ipt_ECN.h
   M include/uapi/linux/netfilter_ipv4/ipt_TTL.h
   M include/uapi/linux/netfilter_ipv6/ip6t_HL.h
   M net/netfilter/xt_DSCP.c
   M net/netfilter/xt_HL.c
   M net/netfilter/xt_RATEEST.c
   M net/netfilter/xt_TCPMSS.c
   M tools/memory-model/litmus-tests/Z6.0+pooncelock+poonceLock+pombonce.litmus
  </code></pre>
  
  <p>I try to use <code>git checkout -- .</code>, <code>git add -A</code>, <code>git stash</code>, <code>git reset --hard HEAD</code>(and <code>^HEAD</code>) and create a new branch, but all of them cannot work, these changes not disappeared.</p>
  
  <p>My system is MacOS(I just want to read code and use git).</p>
  
  <p>git version 2.19.1</p>
  
  <p>Here is a content in .git/config</p>
  
  <pre><code>[core]
      repositoryformatversion = 0
      filemode = true
      bare = false
      logallrefupdates = true
      ignorecase = true
      precomposeunicode = true
  [remote "origin"]
      url = https://git.kernel.org/pub/scm/linux/kernel/git/torvalds/linux.git
      fetch = +refs/heads/*:refs/remotes/origin/*
  [branch "master"]
      remote = origin
      merge = refs/heads/master
  </code></pre>
  
  <p>Those files aren't important for me, but I want to fix the problem.</p>
  
  <p>By the way, There is no matter on my another remote linux machine.</p>