You can switch over to using a dockerfile by updating your app spec to include a dockerfile_path pointing to it.

Your new app spec might look something like this:

name: sample-golang
services:
- name: web
  github:
    repo: digitalocean/sample-golang
    branch: master
  dockerfile_path: Dockerfile

Then update using doctl with this:

doctl app update $APP_ID --spec .do/app.yaml