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Zim is probably the best note taking/wiki software I've ever used. Ability to render wiki syntax, LaTeX, markdown, and even Lilypond notation, create plots, do calculations, version control notebooks, advanced export to html, and everything can be done without touching the mouse. Beats vimwiki in my opinion and might even be better than *gasp* org mode.

github.com/zim-desktop-wiki/zi

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