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Brings to mind Org-Mode from Emacs (which I have no experience with)... there have been attempts at implementing something similar in Vim, eg https://github.com/jceb/vim-orgmode
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SaaSHub
SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives
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I use (and develop) wiki.vim to take notes in neovim. I write my notes in a markdown dialect similar to the Vimwiki format. In my experience, the perhaps most important aspects of a good note taking system are:
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Findability! Ensure you have a simple way of rediscovering old content. I use Fzf to navigate all my notes (:WikiFzfPages) and ctrlsf to search them (with rg as the search backend). In any Vim session, I can type ow to start search for a note.
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zk.nvim
Discontinued Neovim plugin as a lightweight wrapper around https://github.com/mickael-menu/zk
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zeta-note
Discontinued Markdown LSP server for easy note-taking with cross-references and diagnostics.
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neuron
Future-proof note-taking and publishing based on Zettelkasten (superseded by Emanote: https://github.com/srid/emanote)