In deploy.rb you have:
set :shared_files, ['config/database.yml', 'config/application.yml']
and right before deploy do run
run(:local){
desc 'upload shared files'
fetch(:shared_files, []).each do |linked_dir|
command "scp #{linked_dir} #{fetch(:user)}@#{fetch(:domain)}:#{fetch(:shared_path)}/#{linked_dir}"
end
}