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
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.