title: git status shows untouched files as modified, and git diff cannot hash them
body: <p>Ubuntu 16.04, git version 2.7.4</p>
  
  <p>I have been developing some code locally that is also hosted remotely.
  Today, and a few other times earlier occasionally, what follows happens.
  The other times it disappeared after just waiting sceptically, but now it seems to be persistent.</p>
  
  <h3>Step 1, pass: synchronize current branch with remote</h3>
  
  <blockquote>
    <p>git pull<br>
    Already up-to-date.</p>
  </blockquote>
  
  <h3>Step 2, fail: check status and new modified files show up out of the blue</h3>
  
  <blockquote>
    <p>git status</p>
    
    <p>On branch [mybranch]<br>
    Your branch is up-to-date with 'origin/[mybranch]'.<br>
    Changes not staged for commit:<br>
    (use "git add ..." to update what will be committed)<br>
    (use "git checkout -- ..." to discard changes in working directory)   </p>
    
    <p><strong>some 30+ files are given as modified, even though I don't quite think they have been changed</strong></p>
  </blockquote>
  
  <p>(After reboot they have become 15, erratically. 
  After another reboot, 3. 
  Take note: no action on the files)</p>
  
  <h3>Step 3: inquiry what the difference would be</h3>
  
  <p>Probing the situation with a couple of files, I get</p>
  
  <blockquote>
    <p>git diff ../../[directory]/[directory]/[file].md5<br>
    <strong>error: short read No such file or directory</strong><br>
    <strong>error: [directory]/[directory]/[file].md5: failed to insert into database</strong><br>
    fatal: cannot hash [directory]/[directory]/[file].md5  </p>
  </blockquote>
  
  <h3>Research</h3>
  
  <p>Thinking of <a href="https://stackoverflow.com/q/27056788/5459638">Git shows all files as modified after changing file permission</a>, I don't think to have changed permissions any recently. Those files are quite fossilised. </p>
  
  <h3>Questions</h3>
  
  <p>What is the possible cause of this situation, and how to prevent that this happens again?</p>
  
  <p>And why would it self-heal automagically at times, and persist at others? </p>