The Hub

Rather than markdown, I've gone for wiki syntax. In fact, I've built a network around my writing using Raspberry Pi's (little computer-on-a-card that costs less than £35).

A NAS (network attached storage) with (currently) in excess of 6Tb of storage for my novels.
An intranet server which hosts a wiki farm - a collection on wikis running of a single instance of the software.
A VPN server so I can access my novels (and music) from the outside world.
A laptop (also made from a Raspberry Pi) that fits in a briefcase for mobile computing.

There is one wiki that hosts the farmyard, the others (called animals, so yes, it's an animal farm) each host a novel. Wikis have the benefit of keeping a history of any changes I make, so nothing is ever lost. The idea is that once the story is written, I can copy it to Scrivener for final editing. I can, of course, write/edit my novels on my phone now - anything with a web browser will do.

I Use Doku wiki for the farm and animals, and Zim-wiki for notes and other prep-work. Since Zim can run locally, I let it do that, and use SyncThing to keep my desktop computers, network storage and laptop up to date (SyncThing is like DropBox or OneDrive, except it works locally and not in the cloud).