This is my sample appspec.yml
version: 0.0 os: linux files: - source: / destination: /var/www/wordpress/ overwrite: true file_exists_behavior: OVERWRITE
In CodeDeploy default is DISALLOW, so you will get an error if the file already exist in that location.
And this is Updated AWS User Guide for AppSpec 'files' section (EC2/On-Premises deployments only). In there you will find three options, DISALLOW,OVERWRITE and RETAIN.