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.
It's pretty disappointing that Mozilla chose to go with Mastodon. There are already plenty of org-backed mastodon instances. It would have been nice for the supposed primary steward of the web and decentralization to really show the power of the fediverse and use a different implementation. Mozilla, and any other orgs starting up instances, could really help expand the fediverse, instead they're helping to cement mastodon in it's Gmail position.
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.