title: Adding file to git's stage does nothing and cannot be committed
body: <p>I have gotten myself into a bizarre situation where in one of my branches a web.config file cannot be added to the stage. The output of</p>
  
  <pre><code>git add path/to/web.config
  git status
  </code></pre>
  
  <p>Is the same as as before the file was added. Web.config appears to require modifications and has not been added to the stage. </p>
  
  <p>Perhaps more interestingly, when I delete the Web.config from the file system and run <code>git status</code> I get output that indicates I have <strong>two web.config</strong> files that are ready to be deleted and are not staged.</p>
  
  <pre><code># Changes not staged for commit:
  #   deleted: path/to/Web.config
  #   deleted: path/to/web.config
  </code></pre>
  
  <p>Note that one has and uppercase W and the other a lowercase w. The file that I removed on the actual file system is an uppercase 'W'.</p>
  
  <h3>Edit 1</h3>
  
  <p>The output of <code>git ls-files --stage</code> shows that there are indeed two files that differ by case in the index.</p>
  
  <pre><code>100644 63cd5911b9b12bbad559bb69b1b596708b932061 0 path/to/Web.config
  100644 d60ab44bb38f05ffce126ddd3c3293b06e6e4096 0 path/to/web.config
  </code></pre>
  
  <p>I output each of these to a file with <code>git cat-file -p &lt;hash&gt; &gt; &lt;file&gt;</code> and compared the two files. While the textual content is the same, the uppercase Web.config contains CRLF endings and the lowercase web.config contains lowercase endings.</p>
  
  <h3>Edit 2</h3>
  
  <p>With the file physically deleted from the file system <code>git reset HEAD</code> produces this output but the file is not restored on the file system and therefore cannot be added.</p>
  
  <pre><code>Unstaged changes after reset
  D    path/to/Web.config
  D    path/to/web.config
  </code></pre>
  
  <p>I want the file in the working directory to have CRLF as I am working on Windows but I would like for text files to be stored with LF in the internal Git database. So, I assume that would be 63cd591 but I could be off base here.</p>
  
  <p>How do I permanently remove path/to/web.config from the index in this scenario? I am on Windows and cannot have two files on my path that differ only by case.</p>