I use TiddlyWiki via TiddlyPWA. It's an offline-capable PWA with a very quick sync capability. It works beautifully on my phone and desktop. It doesn't have folders, but it does have nestable tags, which works really well for me. I don't think it supports markdown out of the box, but I'm positive you can find a plugin for it. Plugins are crazy simple to install; you just drag and drop a link into you wiki tab and confirm installation.