I use .MD files, helix terminal editor with a markdown LSP called markdown-oxide that replicates the obsidian feature set (like bidirectional links, tags, making new notes automatically, two keys get you from a in-line footnote to the definition and back again, etc), and rumdl which is a super efficient and customizable markdown linter and formatter (semantic line breaks far the win!) . Since it is all helix I can jump around a huge web of interlinked files very quickly with only a few key presses, as well as inside a document and manipulate them en masse or in minute detail all with only a few taps. All of your standard open source terminal tools work with it, difftastic, bat/cat, zoxide/CD, ripgrep, fzf, git, LLMs, encryption, sync, etc etc. I use yazi for a visual filepicker and zellij for tabs. Run it on a server and connect from any computer in the world without downloading a single thing. I sometimes make use of two tools called rucola and tree-md for looking at prettier versions of the texts and seeing stats about how they interact. All open source of course!

There is no better interface for text than a terminal, and we are in the golden age. Despite being extremely powerful, this setup will run on resource constrained machines.