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What's the best way to organize my notes in a plain text

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What's the best way to organize my notes in a plain text file? Is there a standard format or do you just use whatever works for you?
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>inb4 "le plebbit"
but I use Markdown and indentation. To me it's very readable, and obviously more so if I convert the formatting some time afterward.

In terms of structure it's basically like an outline but I try not to go more than three levels deep. Hurts readability.
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>>61964670
I'm currently working on a little program to address this myself. The idea is that I write my notes in a really simple markup language (that I'm also making myself) so that it's easy to type quickly, then the program reads the file and produces a nicely formatted PDF document so that I don't have to spend time going through a nasty-looking plain text file
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