Agreed
If Microsoft Word were to support the Textbundle format, the whole problem would be solved. But that seems quite unlikely.
AFAICT, there is now an option which changes this behaviour (it was affecting indexing and searching as well).
You have to set a hidden preference. Use this in the terminal:
defaults write com.devonthink.dt3 IndexRawMarkdownSource -bool true
Then File > Rebuild Database.
At least, I don’t see duplicates with markdown files containing only Bookends links.
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I would be happy just if Apple supported it 
maybe I missed it - but what app is that?
Agreed; I only use RTF for portability/archiving. MS Word file formats have changed, Claris Works, Apple Works, MacWrite Pro, all have proprietary file formats that require some acrobatics and contortions to import, but RTF is fine.
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Simple: I prefer rich text because I share documents with Windows users without having them complain that I’m not using Microsoft Word.
That’s exactly my point - collaborative writing is extremely common in business, consulting, law, academics, and probably other fields as well.
Come to think of it - other than a personal diary or personal study notes in school, what do you ever write that you do not collaborate on to some degree? If you are writing a novel, don’t you have a few friends who you share it with and solicit comments from?
Actually let me turn it around 180 degrees. I am fully comfortable with Markdown but that said, if someone were to share a manuscript with me for comments, I would most prefer to give my suggestions by turning on Track Changes in Microsoft Word or other compatible software. And I most prefer that colleagues/clients do the same to offer suggestions or questions about my work.
I am certainly not a hardcore Microsoft fan overall and have lost count of how many apps and scripts I have installed on my Mac… but that said, I must admit that with regard to the simple but extremely common task of having someone make suggestions to edit a document and then letting the author easily accept or reject those changes one by one, I do not know of anything better than Microsoft Word.
Can anyone suggest an alternative to Microsoft Word - regardless of whether it uses RTF or PDF or something else - that handles the “Track Changes” workflow better? And even if it exists, how do we get over the near-ubiquitous nature of Microsoft Word in business?
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I sometimes have to license MS Word because publishing depends on it for track changes and comments. I can occasionally get by with using Pages, but some publishing work flows are heavily scripted to import documents from MS Word files using custom templates to InDesign. So yeah, sometimes you must use MS Word.
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I can’t remember to have ever shared something with someone else, who should thereafter be able to alter my text!
And I personally also don’t know anybody, who did so.
And specially if someone is writing a novel, it is, in my opinion, a very bad idea to hand over the text to “a few friends” in a way, that the text could be altered! Give them a PDF, they could easily comment on, but why should they be able, to alter your novel?!
You wouldn’t be able to. MS Word is certainly a capable piece of software but what recommends it most is that “everyone has it” and that it is a standard in the business world without any real competition. I’m a dyed-in-the-wool plain text guy, but I used it for decades at work because that was the expectation.
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I misspoke a bit. I’m using Pages for most of my writing, but because I ran into a scary issue with Ulysses sync on a big book project, I bit the bullet and went back to Scrivener to finish the book. Thus, I’m using Pages and Scrivener. I also continue to use Apple Notes for all meeting and personal notes.
I’ve tried Craft, iA Writer, and Obsidian several times but for reasons I’ve stated here and elsewhere, I have begrudgingly concluded that plain text using markdown is not sufficient or efficient for my needs. In a sense, I’ve come full circle having always used a word processor. Given my many posts, it is a bit embarrassing to have landed where I started before participating in this forum. Yet, I believe the plain text/markdown detour was worthwhile. I’ve learned a great deal that will serve me well over the long run.
Perhaps my odyssey will benefit others. 
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Git is better than Track Changes.
However, as I whined about above, it isn’t exactly trivial to use.
That xkcd made me cackle 
You can experience this yourself at any time by letting a writer produce content for an e-newsletter in Google docs and then copying and pasting in MailChimp 
And these young kids today don’t know how to read html and remove all the stupid formatting they just pasted into their newsletter 
This is exceptionally common in pretty much any office setting that involves report writing or any content production, although the actual method chosen varies. I’ve worked for offices that use Microsoft and offices that use Google, though I personally prefer Google (I hate them as a company but think they handle tracked changes and commenting very well).
In my personal life I am a Markdown person, but I switch to something else when I need to embed images. It happens rarely so it’s not a significant issue for me, but if you embed images regularly I think it’s pointless using markdown, you’re just making life hard for yourself. I had to do it today so it was fresh in my mind, I just switched to Apple Notes as it’s only a temporary file. If I need to write something more permanent with embedded images, I usually just write it in Pages and convert it to PDF (I’ve made a template with narrow margins just for this purpose!).
Since we went on a little detour about office work, for interest if I need to share notes with colleagues that I wrote in markdown, I’ll often just print it to pdf and share the pdf. If it’s an actual work document I wouldn’t have written it in markdown in the first place since my employer doesn’t use it….
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Yes, I tend to embed images in many documents. This is a bit hard to explain but I embed an image of a keynote slide in my speaking notes so I know when to change slides–I don’t use slides for speaking notes. Below is an example from a presentation titled Compassion without Compromise where I quote from Radical Candor. I paste an image of an upcoming slide in my notes in Pages so I know that I need to bring up that slide (or have the AV director bring it up as I speak) when making this point. This is a pain to do with plain text/markdown. It is much faster in Pages.
Sorry, I missed your question. Google Suite handles this better I think, it’s clear what’s a suggested amend versus a comment, and I like that you both get email notifications and if you log into your GDrive you get to see recent comments without opening the files. You can also invite other people not in your Google suite package to collaborate, e.g. freelancers etc.
I really don’t like Google but they designed this well. Even the spreadsheet collaboration is good!
I am not a fiction author so maybe my analogies are poor
But I would much prefer to go through proposed changes and accept/reject/revise them than manually make every change that someone has described in some other way.
Fair enough - that may indeed be a better solution.
It’s surely not Markdown!
So it looks like we are pretty much in agreement that one of the most critical ‘flaws’ of a Markdown workflow is a different kind of interoperability problem - that of other people
This makes sense - echoing previous replies, whenever I need to collaborate I usually turn to a Google Doc or MS word, depending on who I’m working with. To quote Kieran Healy, author of a great short guide to plain text writing workflows (emphasis mine):
But many people use the [rich text] model, and you may end up working with (or for) some of them. In those cases, it is generally easier for you to use their software than vice versa, if only because you are likely have a copy of Word on your computer already. In these circumstances you might also collaborate using Google Docs or some other service that allows for simultaneously editing the master copy of a document. This may not be ideal, but it is better than not collaborating. There is little to be gained from plain-text dogmatism in a
.docxworld.
For those of us using plain text, it is important to make sure our workflow is not causing a significant amount of pain to those we work with, or to ourselves. We may have decided that plain text is The Way To Go, but it would still serve us well to use rich text in a wide variety of contexts instead of doggedly sticking to our ways.
I tend to take a lot of messy personal notes that are mostly just for myself, or that need some ‘clean up’ before they are shared with others - in this case, having them in Markdown isn’t really a big deal since before sending them off I would need to make them comprehensible to another human being anyway.
I have a friend who is in the process of writing a novel with Scrivener - he sends us snippets in a group chat, we send him back messages quoting the original sentence and our thoughts/changes - it works quite well, albeit not something you could do with an editor.
I agree, but this is not a particularly helpful comment in this context 
The point is determining how we can repackage tools that require a great deal of technical knowledge into easier-to-use forms for those that don’t want to be constantly futzing with their tools just to cite something.
I know I, for one, appreciate witnessing your winding journey through the Lands Of Plain Text (and will continue to be slightly amused every time I see a new workflow post from you ). Your thoughts on the pros and cons of these many tools have been very informative. I don’t think there’s anything wrong with picking rich text - it’s certainly a powerful tool, and while nerds like myself like to stick to plain text, I think it does everyone well to see how people work on ‘the other side’ so to speak.
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Thanks for the kind encouragement. As to the “other side, the “dark side,” no doubt!!
Seriously, while my journey has been a winding one, I have learned a great deal, and my workflow is better for it. As one who created a comprehensive technology enhancement plan for my school titled “Deep Learning in a Digitally Distracted World,” there is value in all of my experimentation and resulting frustrations and learnings. I know more about the options and possibilities, which I believe make me a better educational leader. At least that’s my story, and I’m sticking with it; nothing quite like self-generated confirmation bias!
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This is standard practice in both trade and scholarly publishing, A self-described professional editor who who wants to actually revise your text is best avoided. Even back in the 1980s editors marked up hard copy but didn’t change the actual file.