update docs (#555)

* Update doxygen-gh-pages.yml

* reorganise docs folder add ref and a button to switch between dark and light, optimise doxygen

.github/workflows/doxygen-gh-pages.yml

@@ -10,9 +10,27 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: DenverCoder1/doxygen-github-pages-action@v1.3.0
+      - name: Checkout repository
+        uses: actions/checkout@v3
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
+          submodules: "true"
+      
+      - name: Install Doxygen
+        run: |
+          sudo apt-get install graphviz doxygen -y
+          wget https://www.doxygen.nl/files/doxygen-1.10.0.linux.bin.tar.gz
+          tar -xzf doxygen-*.linux.bin.tar.gz
+      
+      - name: Generate Doxygen documentation
+        run: |
+          ./doxygen-*/bin/doxygen Doxyfile
+      
+      - name: Create .nojekyll (ensures pages with underscores work on gh pages)
+        run: touch docs/html/.nojekyll
+      
+      - name: Deploy to GitHub Pages
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
           branch: gh-pages
-          folder: docs/html
-          config_file: Doxyfile
+          folder: docs/html