How do you hide folders on the server from Sitecake only? I'd just want to edit the root index.html and not even copy/backup other folders to the sitecake-temp folder, which it seems to do automaticly.
To exclude certain files/dirs from sitecake you can add .scignore file to your site root with files/dirs stated each in new line (https://sitecake.com/docs/website-integration.html).
If there are other pages in your site root except index.html, you can add those in .scpages file in your site root to tell sitecake not to load it in page manager. Here is more how .scpages functionality works https://forum.sitecake.com/t/page-manager-is-finally-available/630/34
If you want to disable pagemanager all together you can do that in editor.cnf file by adding Pagemanager.init = false.