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.