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I use zim-wiki for my notes. Open-source and stores notes in text organised by folders. I like markdown but actually prefer the simple wiki syntax it uses.

If they need to create a PDF I use pandoc and if I need to move a table to a spreadsheet I just copy the text and use the text to columns from delimiter feature. Not sure if this help you or not.

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Zim’s main drawback in these days is that it doesn’t have its own mobile app, and since it’s not based on MarkDown, you can’t use any existing MarkDown mobile apps with it.

That's true, I think they started looking at creating one but it never got off the ground. From my personal perspective I don't, and can't (I've tried), take decent notes on mobile. On the move I just use a jotter it's quicker and move flexible.

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