Configure git repository on production server with remote source

It may be a vague question, but I can't currently find a good solution in my head. I have a BookStack application running on a company server. To simplify and for security I have a custom .gitignore file which ignores everything except our custom extensions and .env configuration. The idea is that developers can add the production repository as remote source in a directory with BookStack along a mocked database to test it securely. Now, this is fine as long I don't have to fetch from BookStack repository. If I add now BookStack as remote source on the production server it will conflict with the .gitignore on update. Do you have any advice on how I could solve this problem, other than resolving this conflict with each update?