Nearly all of todays file based CMS can use Markdown, all need you to login to access files, the file sync can be done through a decent IDE or an advanced editor, I prefer ftp by Filezilla.
Feature 4, I’m not sure how that should work, I did a quick research to see if todays flatfile cms could auto create links. I couldn’t find any that could. To my knowledge not even Wordpress can do that automaticly, you have to choose the file from the dashboard. The file based cms I’ve used were very simple and no one could auto create links.
I found a blog with a good summary of todays flat file cms: hongkiat.com/blog/flat-cms/. Maybe there is one that has a plugin that can add that feature.