title: Wrong git branch is being referenced during program run
body: <p>I have 2 folders: <strong>mcell</strong> and <strong>mcell_tools</strong>.</p>
  
  <pre><code>/mcell$ git branch -a
    master
  * mcell4_mdl2datamodel
    remotes/origin/HEAD -&gt; origin/master
    remotes/origin/binary_reaction_output
    ...
    remotes/origin/mcell4_mdl2datamodel
    ...
  
  
  /mcell_tools$ git branch -a
  * master
    remotes/origin/HEAD -&gt; origin/master
    remotes/origin/development
    remotes/origin/master
  </code></pre>
  
  <p>Both of these folders are checked out on their appropriate (though different) branches, as you can see above indicated by the *. </p>
  
  <p><strong>Problem:</strong> 
  I have a program inside <strong>mcell_tools</strong> that calls a file inside <strong>mcell</strong>, which outputs text into the terminal. My problem is that for some reason the file inside <strong>mcell</strong> is being called as if <strong>mcell</strong> was checked out on the <em>master</em> branch, not the <em>mcell4_mdl2datamodel</em> branch that I want it to be on. </p>
  
  <p>I'm not very experienced with git, so I might be missing something obvious, but it seems to me that because my program inside <strong>mcell_tools</strong> is checked out on the <em>master</em> branch, the file that it calls from the <strong>mcell</strong> folder is automatically configured into it's <em>master</em> branch as well, instead of the <em>mcell4_mdl2datamodel</em> branch that it says it's in. This seems absurd, so I must be missing something.</p>
  
  <p>To clarify, there is nowhere in the <strong>mcell_tools</strong> program that checks its own branch in order to determine the branch of all other files it calls. I know this because I've been able to run different branches from this program in the past when I was using my machine at work (instead of my home setup). </p>
  
  <p>I know that the <strong>mcell</strong> file is running in it's <em>master</em> configuration instead of the desired <em>mcell4_mdl2datamodel</em> because of the terminal output it produces. </p>