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nb
CLI and local web plain text note‑taking, bookmarking, and archiving with linking, tagging, filtering, search, Git versioning & syncing, Pandoc conversion, + more, in a single portable script.
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I use org-mode, a super-powerful plugin for Emacs (now bundled with Emacs) that provides an amazing list of features, including tagging, outlining, scheduling, todo lists, time-tracking, and much more. It can be used to generate markdown, html, and latex documents, and can be used as a literate programming tool, generating code in a wide variety of languages. All driven by simple, structured, plain text.
As wiki and issues in my one of my repos in markdown.
I use VimWiki in Markdown format. It is portable and lightweight, but at the same time very versatile. If I need to print some of my notes, I use Pandoc to convert it into a PDF (or other format). I also use it in conjunction with zotcite in order to use my bibliographical database from Zotero inside (Neo)Vim.
Zim-wiki, in part because it includes a calendar for journaling, in part because of its plugin architecture, in part because it can export to Markdown, and in part because it's fast.
I switched to BookStack at the start of the year and can recommend it. It has support for markdown and draw.io diagrams.
Have a look at https://github.com/rochus-keller/crossline/, an open source cross-platform outliner with true transclusion; it's very fast also with big outlines.
I use plain text files in a folder, and I sync this folder between all of my devices (desktop, laptop, smartphone) using syncthing. It's awesome!
I store them on my server, some of them that I think can help others I put on my webserver with https://github.com/Cristy94/markdown-blog
I use nb, with git for sync-ing and vim as editor. For annotation on books, I use Foliate's feature for annotations. Then I have some convenience scripts for integrating Foliate's notes into nb for example
There are live markdown render plugins for vim that use your browser to display and even scroll the page along with your cursor in vim.
Trilium notes is great. Lots of formatting options and things like mermaid diagrams built in. https://github.com/zadam/trilium