[1]https://www.williamhern.com/living-in-a-single-text-file.html
[2]http://www.43folders.com/2005/08/17/life-inside-one-big-text-fileI have so, so much to say about how to make this approach work. Please AMA if you have any interest in this.
[1] OK, full disclosure, my main file does sometimes spawn child Markdown files for particular projects. I don't apologize for this! A lot of the challenge around sustaining a useful to-do list over multiple months and years is managing the cruft of your thought. If the document gets too crufty or weedy, it becomes an impediment to thought rather than an aid, and you will let it languish. I have a pretty detailed system for mitigating this risk. Spawning child documents for the weedy stuff + "link" to the child in the main is an important technique here.
(Once we start talking about links you might imagine we could use a wiki, but the most important property of the system is to stay lightweight and at-the-speed-of-thought - I use it to capture requirements during meetings, for example.)