And because of that I can just repeat myself:
I would like to write in rich text because I like to just write and not have to first think about if I had to type a backlash in front of a certain character that happens to be used for Markdown markup. But at some point I switched to Markdown. And this is why:
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Markdown is plain text and therefore scripts easily can alter it in any way I want it to get altered. And, unlike rich text notes, the processing of Markdown notes does not require them to be in the active window, which means Smart Rules can handle the processing in the background.
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While DEVONthink keeps all my notes (and more), the actual note taking for me happens mostly not in DEVONthink. Note taking means for me first of all a fast, at best single click/tap way to jot. I do a lot of note taking on mobile devices. And on these devices the majority of note taking apps—at least to my knowledge—don’t use rich text. I use Drafts which even runs on the Apple Watch.
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Footnotes! Footnotes! Footnotes! Apple did not implement RTF footnotes but invented the RTF package format RTFD. And lost interest in it again. RTFD is a dead end, limited to some apps on Mac only, not even supported by the present version of Apple’s very own Pages anymore. My main writing app is Scrivener, which, despite it is a rich text app, imports Markdown files with footnotes without any problem. It’s actually even better than without any problems: Scrivener even distinguishes between “standard” Markdown footnotes and MultiMarkdown’s inline/random footnotes and splits them into footnote and endnote streams. So: Endnotes! Endnotes! Endnotes!