Can I make the main file aka hompage of my website index.md?

Is is possible to make index.md the main file of my project aka the homepage?

Nope. Index.html is what you gotta do. If it is a node.js site, I suppose you could use markdown it and routes (you could use markdown-it on a website, it works fine.) Or just use regular html + css

You can use docsify

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Yes you can, with a little extra work. You can install a package like markdown.js and parser file to HTML and send that as the homepage.