Moonshine is supposed to keep the file in the shared folder and symlink it to the file under current project folder just by adding one line to the config/moonshine.yml
For some reason it created the symlink but it did not upload the file. I had to manually do it by :
on my laptop. On initial setup it actually worked for database.yml. I think it is because of cap deploy:setup command. Remember to add the config file to the .gitignore file so that it does not get checked into the repo.