Deploy a site to GitHub Pages from multiple branches using GitHub Actions

I’ve been moving many repositories over to GitHub Actions to automate deployment and testing. One of my projects uses GitHub Pages, but includes data from two different branches:

The main branch contains the bulk of the website
The app-challenge branch contains a second site that appears under a /heleon/ path

Using GitHub Actions, I set up the site pull from both branches before deploying. The script looks like this:

name: Deploy from two branches

on:
  push:
    branches: [main]

jobs:
  build:
    runs-on: ubuntu-latest

    steps:
      # Checkout the `main` branch
      - uses: actions/checkout@v2
      # Install Node.js
      - uses: actions/setup-node@v2-beta
        with:
          node-version: '14'
      # Install npm dependencies
      # (similar to npm install)
      - run: npm ci
      # Run code to build the site files inside the `big-island-buses` folder
      - run: npm run build

      # Checkout the `app-challenge` branch
      - uses: actions/checkout@v2
        with:
          ref: app-challenge
          # Put the checked out files inside the `big-island-buses/heleon` folder
          path: big-island-buses/heleon
          clean: false
      # Delete the .git folder from `big-island-buses/heleon`
      # This turns the files into a plain folder instead of a git repository
      - run: rm -rf big-island-buses/heleon/.git
      # Deploy the `big-island-buses` folder to GitHub Pages
      - uses: peaceiris/actions-gh-pages@v3
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          publish_dir: './big-island-buses'
          user_name: 'github-actions[bot]'
          user_email: 'github-actions[bot]@users.noreply.github.com'

The first sequence of steps checks out the main branch, installs Node.js and npm dependencies, then runs the build script. The files created by the build script end up in a folder named big-island-buses.

The second sequence checks out the app-challenge branch, and places the files inside a folder named heleon, which is a subfolder of big-island-buses. These files are static so they don’t have a separate build script.

However, putting one git repository inside another like this creates problems for the GitHub Pages script. Deleting the .git folder turns the git repository into a plain folder.