title: Git is not picking up my changed files
body: <p>I'm trying to create a new branch which contains a different version of my project. Unfortunately the newer version's files, while they have different contents, don't get noticed by git as changed and can't be committed. </p>
  
  <p>The folder\files are nearly identical and were placed into the directory at the same time from a backup. The contents of some files are different and I need these changes reflected in a new branch.</p>
  
  <p>By way of example, take this simple mockup I've tried using 2 text files.</p>
  
  <p>File structure: </p>
  
  <pre><code>project/
  ├── older/
  │   ├── File 1.txt
  │   ├── File 2.txt
  ├── newer/
  │   ├── File 1.txt
  │   └── File 2.txt
  </code></pre>
  
  <p>Structure is similar for my actual project, just with a lot more files and subfolders.</p>
  
  <pre><code>Mr JF@Computer MINGW64 ~/Desktop/testproject (master)
  $ git checkout master
  Switched to branch 'master'
  Your branch is up to date with 'origin/master'.
  
  Mr JF@Computer MINGW64 ~/Desktop/testproject (master)
  $ stat -c "%y %s %n" *
  2018-03-15 15:43:35.764654900 +0000 15 File 1.txt
  2018-03-15 15:43:35.765656300 +0000 17 file 2.txt
  
  Mr JF@Computer MINGW64 ~/Desktop/testproject (master)
  $ git checkout -b newerbranch
  Switched to branch 'newerbranch'
  </code></pre>
  
  <p>I copy the newer version of File 1 &amp; 2.txt into the repository here, then:</p>
  
  <pre><code>Mr JF@Computer MINGW64 ~/Desktop/testproject (newerbranch)
  $ git status
  On branch newerbranch
  nothing to commit, working tree clean
  </code></pre>
  
  <p>What's going on here?</p>