title: PhpStorm and pre-commit hook with PHP-CS-Fixer which modifies number of blank lines in php file
body: <p>Reproduces on Windows and Mac OS.</p>
  
  <p>In our project we have pre-commit hook which runs <a href="https://github.com/FriendsOfPHP/PHP-CS-Fixer" rel="nofollow noreferrer">PHP-CS-Fixer</a> which modifies number of blank lines between methods in file (reduces from many to one). After that it makes <code>git add &lt;modified_file&gt;</code> to stage that change.</p>
  
  <p>When we commit from PhpStorm Commit Dialog (<kbd>Ctrl + K</kbd>) it successfully commits and then causes strange state of that dialog (press <kbd>Ctrl + K</kbd> again after commit) with message "Contents are identical" (see first screenshot).</p>
  
  <p>PhpStorm commit dialog after commit with blank lines modifications</p>
  
  <p><a href="https://i.stack.imgur.com/RKMeD.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/RKMeD.png" alt="PhpStorm commit dialog after commit with blank lines modifications"></a></p>
  
  <p>What we see if run <strong>git status</strong> after commit</p>
  
  <p><a href="https://i.stack.imgur.com/eNOIy.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/eNOIy.png" alt="What we see if run **git status** after commit"></a></p>
  
  <p>What we see if run <strong>git diff</strong> after commit</p>
  
  <p><a href="https://i.stack.imgur.com/LLNRh.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/LLNRh.png" alt="What we see if run **git diff** after commit"></a></p>
  
  <p>Note: If we commit from command line (not from PhpStorm commit dialog) all goes OK.</p>
  
  <p>(<strong>UPDATE</strong>) Note 2: If pre-commit (php-cs-fixer) make change not related with blank lines all goes OK as well.</p>
  
  <p>What we doing wrong? Is it a problem related to how PhpStorm commits? How to fix that?</p>