title: Why is github separating my library files from their original directory?
body: <p>This is an android studio project, and a while back i had some package naming issues when i created a new Library module. Somehow github split my library source code paths, yet my local repo shows everything as it should be:</p>
  
  <p>As you can see in the screenshot of my local repo, all code related to my Toolbox library is within the toolbox path. in github however, toolbox/src is housed in the root project directory? </p>
  
  <p>LOCAL REPO (correct file structure):</p>
  
  <p><a href="https://i.stack.imgur.com/jtVPa.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/jtVPa.png" alt="Snapshot of my local repo"></a></p>
  
  <p>REMOTE REPO (incorrect file structure)</p>
  
  <p><a href="https://i.stack.imgur.com/6r5dw.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/6r5dw.png" alt="Snapshot of my local repo"></a></p>
  
  <p>I've tried creating a new remote and pushing to that, but i get the same problem. Note that any new commits i make are placed under the Toolbox directory where they should be, just older files are stuck.</p>
  
  <p>Here is a link to the remote if you'd be willing to look at it for me. I think this has something to do with my package clashing issues i had at the time i commited. I was getting a gradle error saying multiple dex files were found for /BuildConfig. I would highly appreciate any insights or wisdom, and how to prevent this in the future. Thank you stack. If you want any more details on my problem i'll absolutely include them. Thank you!
  <a href="https://github.com/whompum/BonitaToolbox" rel="nofollow noreferrer">https://github.com/whompum/BonitaToolbox</a> </p>