Use Jekyll 3 with GitHub Pages - lmmx/devnotes GitHub Wiki

  or for HTTPS:

(NB ensure you have `.git` in your `.gitignore`, I don't know how recursive `.git` directories would be handled)

* Move down into the `_site` (generated static site) subdirectory and initialise a git repo for it (really only *re*initialising the existing repo on the organisational remote repo)

  You'll see `Initialised empty Git repository in path/to/{*}.github.io/_site/.git/`

* Set this fresh `.git` up with the remote URL of the original repo (if HTTPS, change the URL as above)

* Step back up to the Jekyll site: `cd ..`

If at any point `_site` was tracked (i.e. if at some point in time the `_site` directory has not been declared in `.gitignore`) then you may have to run `git rm -rf _site`. You will receive a `'_site' already exists in the index` error when trying the `git submodule add` command if so ([via StackOverflow](http://stackoverflow.com/q/20929336/2668831)).

* Add the `{*.github.io}` site as a submodule of this parent local git repo in the `_site` folder, using the `-f` flag because you're forcibly adding a path in the `.gitignore`.

  * you should see `Adding existing repo at '_site' to the index`

* Git has now added a `.gitmodules` file in the parent repo (or "[_superproject_](http://schacon.github.io/gitbook/5_submodules.html)") - containing the references for the `_site` submodule (pointing to the `*.github.io` repo).

* The submodule needs filling with the remote now (i.e. the original superproject) (see [e.g. SO](http://stackoverflow.com/questions/5828324/update-git-submodule-to-latest-commit-on-origin)). First run:

   to add the submodule repository URLs to `.git/config` ([via Scott Chacon](http://schacon.github.io/gitbook/5_submodules.html)). The head is now detached so you're not working on a branch - specify it and grab the code from remote (_assuming you're using master branch, NB [you won't be](https://help.github.com/articles/creating-project-pages-manually/#create-a-gh-pages-branch) if it's a project GitHub Page_):

   The submodule is now up to date with the `origin master` branch, and you want to discard everything above it.

* I used `git filter-branch --subdirectory-filter _site -- --all` to move all the files in `_site` up to the parent within the submodule (until now you've just put a copy of the whole Jekyll project inside itself under `_site`), and clean out the rest of the (submodule) repo. It did that, but then I was prompted to `git pull origin master`, which resulted in an apparent reversion to the original organisation. If you have all the Jekyll files then there's no need to pull here.
* At this point there's an odd-looking setup with branches, but it's nothing to worry about. I attempted to commit and push the changed refs, then `git pull origin master` as prompted, but there is no need to.
* Do this however you want to, but just retain the `.git` and `_site` folders from what was in the original repo, deleting everything else, then shift the contents of `_site/_site` out into just `_site` (i.e. make the submodule just contain the static site files). I did so by putting them in the parent and removing everything in the submodule, then bringing them back down <sup>([note RE: file deletion](http://unix.stackexchange.com/q/77127/89254))</sup>:

* Everything's looking good finally, so you can now build your site, files will be generated in `_site`, and versioned separately from the submodule there.