Set subdirectory as website root on Github Pages

Somehow for me, the accepted answer only runs the first time. Re-doing it throws errors.

I solved it by running the commands below:

git checkout --orphan gh-pages
git --work-tree build add --all
git --work-tree build commit -m 'gh-pages'
git push origin HEAD:gh-pages --force
git checkout -f master

There is a detailed gist with all the required steps.

The gist is here:
https://gist.github.com/cobyism/4730490

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From the gist

Deploying a subfolder to GitHub Pages

Sometimes you want to have a subdirectory on the master branch be the root directory of a repository’s gh-pages branch. This is useful for things like sites developed with Yeoman, or if you have a Jekyll site contained in the master branch alongside the rest of your code.

For the sake of this example, let’s pretend the subfolder containing your site is named dist.

Step 1

Remove the dist directory from the project’s .gitignore file (it’s ignored by default by Yeoman).

Step 2

Make sure git knows about your subtree (the subfolder with your site).

git add dist && git commit -m "Initial dist subtree commit"

Step 3

Use subtree push to send it to the gh-pages branch on GitHub.

git subtree push --prefix dist origin gh-pages

Boom. If your folder isn’t called dist, then you’ll need to change that in each of the commands above.

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If you do this on a regular basis, you could also create a script containing the following somewhere in your path:

#!/bin/sh
if [ -z "$1" ]
then
  echo "Which folder do you want to deploy to GitHub Pages?"
  exit 1
fi
git subtree push --prefix $1 origin gh-pages

Which lets you type commands like:

git gh-deploy path/to/your/site

Since August 2016 you can use /docs subfolder of the master branch for your sources.

So if you can tell to your site generator to use /docs in place of /build you are done (without subtree).

Note: As pointed out by @thislooksfun in the comment, this is valid only for project pages (like <username>.github.io/<projectname>), but not for user or organization pages (like <name>.github.io).