I am trying to override the main index.html the one that base URL uses. I tried creating content/index.md when I do these other pages don’t render and the menu generated by the Hugo doesn’t show in the index.html
If I remove index.md and replace it with _index.md it workes fine but then as per the documents _index.md refers to _default/list.html and index.md refers to _default/single.html, but adding the loot index.md changes the structure of the website.
Your theme has a index.html file but, there’s no reference to {{ .Content }}, which is needed to pull content from the body of a markdown file.
Override the theme’s index by copying the theme file to the same place as in your project folder, and editing it. If Hugo finds a non-theme file in the same location as the theme file, the non-theme file gets precedence.
Copy the theme index to /layouts/index.html then edit to override.
Since the themes are in git repos that can easily get overwritten, I would recommend doing the override thing I mentioned above, over editing the theme directly. Of course, you can always copy the theme’s files in, instead of doing a git clone.