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+1 for VimWiki, it's just simple enough for decent note-taking although it's not as highly customizable as org-mode. Btw, I think the internal linking features and others do not work with Markdown syntax of VimWiki after the export, or have you figured out something ?

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I haven't had a chance to integrated vimwiki into my school notes just yet. I havent used the export function in vimwiki yet, as I stick with viewing my notes in vim.

I'm not sure if HTML outputs the paths the same way that the vimwiki does, could you possibly use relative links or something? I can't get HTML conversion to work for me right now for some reason. You could also possibly compile all the notes at once, and use sections to refer to certain files. Similar to how LaTeX outputs sections.

I haven't tried using links after an export before. One thing to check might be the source code of the exported file? That might give you a hint of where the exported page is looking for its link targets.

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