I'm sure there are special cases where residents would need bathroom access directly from their apartment, but are there any good reasons for private bathrooms, other than convenience?
To me, one of the most interesting things about converting non-residential building to residential is the potential for different ways of living. A shared bathroom and kitchen with offices surrounding a communal area could lead to a more communal lifestyle for residents.
I use TiddlyWiki via TiddlyPWA. It's an offline-capable PWA with builtin sync and encryption. It doesn't have folders but it does have nestable tags. I don't think it supports markdown out of the box, but I'm positive you can find a plugin to use markdown. Plugins are crazy easy to install in TiddlyWiki; you just drag and drop the plugin into your wiki window and confirm the installation.