The easiest solution how to publish with Hugo to Github Pages is to have two separate repositories, one with blog source files and second with html files. Simple.

We can push files from both repositories manually or can do better. Push just source content and leave the rest for automatic deployment. I did not know about Wercker until read automated deployment tutorial on Hugo site. And with hint from Skarlso post, that process became so easy.

Steps:

1. Create new application on Wercker with Hugo source repository. Leave the recommended settings.
2. In Workflows add new Pipeline with both names set to deploy.
3. Create new Personal access token on Github, and copy its value to Wercker Environment, with key name: GIT_TOKEN.

4. Add wercker.yml to your Hugo source repository. Just change your Github name.

   box: golang
   build:
       steps:
           - arjen/hugo-build:
               version: "0.19"
   deploy:
       steps:
           - install-packages:
               packages: git ssh-client
           - leipert/git-push:
               gh_oauth: $GIT_TOKEN
               repo: <name>/<name>.github.io
               branch: master
               basedir: public
   
   

5. Push and enjoy.

Note that in arjen/hugo-build I do not use theme option, I have all layouts and static files in my hugo-blog. For more info go to arjen docs.