Pushing Documentation to Github Pages

.gitignore

# ignore built md and html files in the slides directory
slides/*.html
slides/*.md
slides/fig/*
slides/figures/*

citation.md

Reference: http://ricostacruz.com/lidoc/manual/guides/uploading_to_github_pages.html

deploy.sh

# Makefile
GITHUB_REPO ?= yourname/project

# Sends the documentation to gh-pages.
docs.deploy: docs
  cd docs && \
  git init . && \
  git add . && \
  git commit -m "Update documentation."; \
  git push "git@github.com:$(GITHUB_REPO).git" master:gh-pages --force && \
  rm -rf .git

.PHONY: docs.deploy

I tried this and it works. Basically it works by initializing the deploy directory as a git repository, pushing it to a remote gh-pages branch (by force) and removing the .git directory so that all history is erased.