I would add a README file under
then force the file to be added to the repository by executing
git add -f sites/default/files/README and push your files.
-f flag will allow the file to be added by overriding your
The next time you clone the repository on a new location the folder
sites/default/files will be created by git.
When downloading Drupal the sites/default folder contains a file called default.settings.php. And one solution here would have been to add that file. But since your .gitignore excludes
default.settings.php file wont be added and Git will not add empty folders to the repository.