title: Missing application.yml file - Atom hiding vcs ignored files
body: <p>I am using Figaro to set up ENV variables. Ever since installing it, my <code>application.yml</code> has disappeared. When I do a search for the file in my editor, all that comes up is the reference to the file in my <code>secrets.yml</code> file to ignore <code>application.yml</code>. However, when I go to create a new <code>application.yml</code> in the config folder, it says that <code>application.yml</code> already exists.</p>
  
  <p>I can see it in the finder as well.</p>
  
  <p>I uninstalled Figaro and it still didn't come back, so now I'm not even quite sure it's absolutely connected to Figaro.</p>
  
  <p>Any ideas? I'm happy to set up ENV variables manually, to try Enviable or another gem, but I'd like to find out what is causing this issue.</p>
  
  <p><em>This question has been edited to show that the problem is with Atom and not Figaro, please see Zhurora's answer.</em></p>