title: Repository Structure to patch upstream downloaded sources
body: <p>i have a web application. The application has two sources of code:</p>
  
  <ul>
  <li>source1 - is a released java web application, that must be manually downloaded via a login-protected web ui</li>
  <li>source2 - are modifications and additions (xml and txt) to source1</li>
  </ul>
  
  <p>The finished application is a combination of source1 and source2. Source1 being overwritten.</p>
  
  <p>Source1 is code that I do not touch. It is released as a zip file that i have to extract. Every few months there is a hotfix (also zip). After half a year there is a new major release. Major releases are incompatible so every half year I would have to save the old version and start anew.</p>
  
  <p>Source2 is code that I modify or includes additions ot source1. Source2 is continually developed and changed.</p>
  
  <p>I would like to use CI/CD to build the finished application and deploy it
  on a server. I would like recommendations on how I should best structure my repository/repositories?</p>