Workflows with Markdown

I usually write in plaintext files (.md, .txt) through WriteMonkey3, Obsidian, Typora, FocusWriter etc.

However, for organisation, planning and creativity I like to play around in Timeline, Plottr, Mindomo, Excel etc. Which leaves me with a workflow problem. I’ve looked up export and import formats as follows:

Import Export Sync
Mindomo .txt, .md, OPML, Excel, Mindomo file (.mom, .pmom) MindManager file (.mmap) Freemind file (.mm) Mindmeister file (.mind) XMind file (.xmind) file (.xml) SimpleMind file (.smmx) iThoughts file (.itmz) .txt, .md, OPML, Excel, Mindomo file (.mom, .pmom) MindManager file (.mmap) Freemind file (.mm)
Plottr Word, Scrivener on roadmap Word, Scrivener
Timeline .csv .csv Scrivener, Ulysses
Excel .csv .csv
Scrivener .txt, OPML, Word, .md, Word, OPML

If I put in a lot of detail, I want to be able to push it into markdown files for use when writing. Mindomo will do that directly, otherwise it looks as if I will need to use Scrivener as a converter.
Plottr doesn’t import from anything yet. It exports to Scrivener, which can sync with Timeline.
Timeline can import and export from/to Excel via .csv (and thence Mindomo).

There are other conversion methods, but it’s a pity that workflows will have to be so convoluted. It looks as if I can start anywhere I want, but will then have to think things out. Will become simpler when Plottr can import.

I’m also not sure how much it will matter. So far I’ve only used any of these tools for a single purpose. But what I will want to avoid fleshing things out in any program that doesn’t give me an easy route to putting the info into my .md files.

Hi @Dormouse,

It seems you have a lot of options there in terms of software for writing and planning/ outlining. I also prefer to write in plain text files and use Ulysses as my main writing program. Not only because it is markdown based, but because, in my opinion it is at least as good as Scrivener for long/form writing projects, if not better, and also has extensive built-in blogging support. Matching Ulysses with Aeon Timeline is the sweet spot for me.

However, I appreciate your needs may be different to mine. Ulysses’ sync with Aeon can push metadata through to keywords or to the app’s notes system. I have tweaked my system to have just enough metadata stored in Ulysses to facilitate my writing. But I also know that Aeon Timeline is close by should I wish to look some important information up. And on iPadOS, with the new multitasking workflows the whole system works like a dream. I have put in a feature request for x-callback-urls to be able to access Aeon directly from within Ulysses and that request is to be considered.

I also use DevonTHINK for research and Aeon Timeline is my bridge between my research material and my writing in Ulysses. All facilitated through x-callback links stored in Aeon Timeline’s attachments panel.

You may be a markdown purist re metadata. I know Obsidian stores pure Markdown metadata in its headers. But could you see yourself using Ulysses? Coupled with Aeon Timeline it’s a great combination.


Love plaintext, hate markdown. But it/they is/are what there is. I only use very simple syntax to avoid too many variant problems, and even then I use wikilinks, which aren’t standard markdown (yet).
But I am a files purist. I don’t like to store anything in a database except temporarily.

Not an option since I’m not on a Mac. And iirc, it’s markdown in a database which would rule it out for me again.
Admittedly, most of my writing is done in WriteMonkey 3 which keeps everything in a .json database (enabling wonderful folding control) but I’m okay with that because it also keeps all my data in synchronised files. Which are simultaneously shared with other apps like Obsidian and ProWritingAid etc. Sometimes I might swap backwards and forwards between programs on the same file.

I never took to Scrivener. Tried it from time to time, but it never flowed. I like the company, keep licences up-to-date but don’t like using the program itself.

I put my research etc in markdown files that I access through Obsidian. The wikilinks are virtually instant, and the mix of links and backlinks makes it very easy to analyse what I have. Also have various simple kanbans in Obsidian for a bit more organising and linking.

I’m impressed that you switch easily to Timeline to look things up. I find that too big a discontinuity most of the time. It’s the very different interface probably; doing something bigger is fine, but something small is an irritation when I can get it with a couple of clicks when it’s in Obsidian. I don’t use my iPads, but Obsidian works well on my Android tablets.

The planning and creating ones are important. I’m never completely convinced it’s not just inefficient procrastination and I would really be better off with just one, but I find them all different and I make progress in one, when I don’t in the others. At times I even use a simple outliner. It’s whatever helps me best to sort things out in my head.

Apologies, I hadn’t understood that you were on Windows. As you hadn’t pointed out which platform you were on, I had a very brief look at WriteMonkey’s web page and saw a screenshot of a Mac application.

Hi Dormouse,
To turn the question around a little the other way… what would be your ideal workflow?


No need for apologies at all. I’m interested in workflows on any system, and would probably use DevonThink and trial Ulysses if I did have a Mac.

But Apple and I have a philosophical disagreement.
I think I’m safest being free to go anywhere.
They think I’m safest if I’m contained in their bunker.
They think they know best; I think I do.

As it stands, I can switch easily between Windows and Linux with most of my usual programs and would be able to on Mac if I had one.

Yes, I also have persuasions towards this point of view. I am an ex Linux user. I loved the true freedom that brought with it. Unfortunately I just could not find enough high quality software on that platform, and I could never bring myself to return to a Windows based system, so I migrated across to Apple quite some years ago now. And it was the best thing I ever did. I have Ulysses, Aeon Timeline, DEVONthink as the huge benefits to offset the downfalls of being at Apple’s behest.

But we are each to our own and I am sure that the Linux ecosphere has now spawned quite a few decent pieces of software for writers. But I like my current toolset too much.

If you are interested in the workflows of others, you are welcome to check my essential tools out under The Write Tools at

This is a very interesting question (at least to me). It will take some thinking about: usually I just adjust to how things are rather than speculate on what would be perfect.

It’s complicated by the fact that I do many different types of writing with different needs. Fact, fiction, formal reports, academic, even journalism at times. All they have in common is that they have subject matter, and a written output where elements are pulled together in threads. Not one answer, maybe then.

  • I use Mindomo to play with ideas and relationships. It’s not always my first stage - often I’ll come to it (or similar techniques) to work things out after making a start.
  • Plottr seems designed for pulp fiction series; I use it to help structure sections and chapters, watching elements and themes across the narrative.
  • I use Timeline only when there’s a timeline that matters.
  • I use Excel, partly because I’ve used it for a long time before these other programs existed, but also because it’s a quick and easy way to write structured info.

This makes them all appear very different when they actually have elements in common. If there is a character, then they each invite a description of that character and stimulation to embellish that description. But I don’t want a description spread across three locations, especially when I really want all of it in a fourth.

So, my ideal workflow for that would be that they import/export/synchronise those fields with an originating markdown file.

Do I need more? Not especially probably.
I’d like them to exchange data easily, so that it travels with me when I switch programs. .csv ought to be good enough for that; I’m okay running .csv through Excel for the program that requires .xls/x. OPML too, but that’s less spotted.
So I can see how to do it, but the method required appears to depend on the precise A>B at the time.

I find Windows much improved. Gates matched Jobs for avarice, and Ballmer was a shouty disaster, but there has been improvement since.

That’s the problem for Linux. It’s best programs, usability-wise, tend to be cross platform, and there are many areas where it doesn’t have a good solution. It contains all the advantages and disadvantages of an open-source philosophy. A tendency to expect everything to be free and a keenness to fork at the drop of a hat. The drift to web apps is changing the environment though.

Apple offered developers the advantage of a captive high-paying market which encouraged the growth of a small number of very high quality programs. I understand the attraction, but have always been wary of lotus eating.

I’ll check out your website.

Drifting a long way off topic, but when I first started working on Aeon Timeline, Apple offered something much more valuable than that: an ecosystem of users who respected and appreciated indie developers, and an operating system who nurtured that because they understood it was something that set them apart from Microsoft. Apple’s developer tools were free when Microsoft was still charging thousands of dollars.

The App Store is something I accept I must live within rather than something I truly embrace. It probably has led to some increased market exposure for the app ecosystem in general, as it has led to more users who are reminded that “there is probably an app for that”… but it has also driven prices and perhaps quality down in the process (good apps take years to develop, and the App Store model does not encourage that investment).

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One of the things we are aiming to do with Aeon Timeline 3 is unify some of those tools a little bit with the introduction of the Narrative and Outline views for mapping those chapters and scenes, and Mindmap View for that initial idea sketching.

We are aiming for the experience of “Create the data once, and it is available everywhere”, rather than chopping and changing between different apps and trying to pull it all together.

So again, this is perhaps a different topic, but I would be interested to understand any gaps in those features within Aeon Timeline 3 that are better covered by Mindomo or Plottr, so that we can help unify that whole experience.

I guess understanding what format that Markdown file should take would be a challenge.

I could picture it being relatively easy, for instance, to take a Timeline Narrative and turn it into markdown – each step down the tree using progressively smaller headers, with perhaps the item summaries being included as text in between that you could then extend into your writing.

Pulling back out of that structure may be a little more difficult though.

The benefit of markdown is that it is text based and yet still potentially hierarchical.


So true. And now Microsoft are heavily supporting open source developers and Apple erect little barriers between ‘their’ apps and other OSs.
Pure corporate strategy for all of them.

I’ll look out for that. I haven’t spent much time using the beta since nothing I was doing needed a timeline, and I’m not really in a position to comment yet.

Some things may be pure usability and personal preference. When I was checking out mindmap programs, I trialled all of them (have done periodically every half decade or so) in some depth. Mindomo was the only one I’m happy to use, and yet it doesn’t really look so very different to some of the others.

I’m probably in a position to start working on it now. Couple (more than a couple) of projects that might suit. I’ll keep you in touch.

I’m not sure there’s much overlap between Timeline’s features and the way I use the other programs. Mindomo is a very freeform playing with nothing crystallised; could be a source for Timeline, but it seems unlikely I’d replace it with Timeline.
Plottr is very visual and mouse friendly. I can see potential overlaps (eg scenes and character & tag filters). It is set up for series, which Timeline isn’t (and that’s not relevant to me anyway). An initial glance at a Timeline import from Plottr (via Scrivener) seems okay only up to a point - no characters etc; can’t test in the other direction since Plottr doesn’t have an input yet.

I’m assuming that a Timeline export via Scrivener to md will work, but I haven’t tested that yet.

I see the problem. I’m most interested in the information in Characters, Places, Arcs and Themes being synchronised. Events too. Timeline not so much since that will be much better presented in Aeon Timeline.

Feel free to put together the type of format you would like to see, and we can see if it is something that might have general appeal.

Markdown is pretty simple, so a markdown export would be relatively easy for us to implement. The challenge is just working out a format that will satisfy enough users to warrant the effort.

I imagine we would definitely include a Markdown export of the narrative if we were to do it, because it makes a lot of sense to me to build a timeline, then construct a narrative in Aeon Timeline planning out your story, and then export that in Markdown so it can be pulled into another writing app to produce the actual text.

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Potentially yes. But not necessarily. A narrative needn’t tie in with a timeline of events - for instance, if I were writing a report on something with a timeline, the report structure would likely be very different. Ditto histories. But it would usually be true in fiction.

The intent of the Narrative and Outline Views is that they are an independent structure and order from the chronological/timeline events, so I would expect the narrative would be a useful thing to build on your way to a markdown layout regardless of whether it is fiction or non-fiction, and closely connected to the timeline or not.

Of course, this will vary for different user’s preferences and workflows, and the exact nature of work, etc. but we are aiming to create something that is quite flexible in that regard.


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OK. Thanks. I’ll remember this when I’m testing those features.

I’ve had a look and compared it to Plottr.
Plottr is much more visual and freeform; Timeline is more structured.
Depending on what I’m doing, I’m likely to have a strong preference for one or the other.
Further thought: I think Plottr would work for pantsers, Timeline not so much.

Thanks. I had a look at your site. Seems we both use ProWritingAid.
In terms of craft, having seen the books you list as being helpful and knowing you use Aeon Timeline, I suspect you fall on the planner part of the spectrum. In which case I’d recommend one, or both, of Steven James’ books (Story Trumps Structure, Troubleshooting Your Novel). He writes as a pantser and even makes sense of it, which can add an extra dimension to inveterate planners/plotters.
Not that I agree with everything he recommends, of course.