I have data stored in Apple Notes, Ulysses, and Bear to name a few. I also have data stored as individual files some of which are indexed in Devonthink and also accessed via iA Writer, The Archive, and 1Writer to name a couple. I would like to settle on one method and stick with it.
What is your preferred method and why?
Individual files by a mile.
Why is it important to have one method and stick to it?
I use Notes (for personal stuff & ease of sharing with my wife), Ulysses (for most note taking and writng) and DT (for occasional md files which usually get moved to Ulysses). I use Drafts for starting stuff and searching once in a while but not for anything permanent. I rarely use plain text or other text files anymore, though I have a lot which I tend to move on an as-needed basis. The combo works for me and Iâm not tempted to mess around trying other systems.
The main reason is to make it easier to find things.
Plain text files all the way for me. I can use the same folder of notes (synced via a cloud service) on any machine or on the web, theyâre readable no matter what, and I can use them simultaneously in multiple apps that have different strengths (as long as they work with plain text files).
If you use markdown, you then have to grapple with the fact that they all use slightly different flavors of markdown. But some apps even have workarounds for that, letting you make custom syntaxes (so I can highlight with {==CriticMarkup==} or ==other== ::highlight:: syntax as I wish.
Fwiw, I often create my notes in Drafts, in part because it does allow custom syntaxes; then I have actions to file notes to my notes folder as plain text files.
I also capture and create in Drafts. Nothing stays in Drafts. Everything gets acted upon with an action.
DEVONthink 3 every time. No contest from my point of view. Bit of a learning curve but well worth it. I have found my stuff is way more accessible, searchable and âfamiliarâ to me in that app. I canât fully explain why that is to be honest.
I think it depends on whether this is âcoldâ storage or not. I keep all my âcoldâ storage in Finder folders. If I only need to poke around for something occasionally I donât mind the extra time it takes and I prefer Finder as the simplest solution (though I could index the files with Devonthink for increase search power). All my my active stuff that needs to be quickly referenced is in Devonthink, when I close a clientâs file, it goes to the Finder.
I keep my files in an iCloud folder. Itâs (mostly) a mixture of iThoughts mind maps, PDFs, Word documents, PowerPoints, emails and Markdown.
Currently I use EagleFinder to index them - it works well and handles Outlook emails (which I have to use for work) properly which DEVONthink doesnât.
By keeping them as files in a folder, I can switch to other tools as and when necessary, and use the right tool for the job.
I donât care much where my data is â though Iâm meticulous about hierarchical structures in the file system and in datdabases. I use FoxTrot. pro to index everything â so that I can find everything. There is a few exceptions of course â Apple Notes, for one. Spotlight doesnât even find things in Notes.
What was that thing about the wonders of apps designed to Appleâs standards?
Eagle Filet is an amazingly good tool for archives â it will invest pretty much anything. Great for cold storage, because inevitably I will need to find something.
+1 for EagleFiler!
(I think thatâs what you meant. But I will check out âEagle Filet,â too. Sounds like it might be really good at slicing and dicing my info! 
).
Individual files in as few formats as possible (txt, pdf, md, odt, ods, scriv, png, jpg, raw, mobi, azw, epib) cover nearly all of what I keep. What is in databases are indexes to those files, LightRoom, BookPedia, CDPedia and Obsidian to name a few
Reasons:
No vendor lock in in formats or access
control of security and storage location
Cross platform options for future use (in my cse Mac and Linux are all I care about)
Interesting. It is all very well talking about ânon proprietaryâ stuff. It turns out to be a lot more obscure than one might think? Especially for those of us less involved and knowledgable âunder the hoodâ as it were.
And, like you, I am not so concerned about what are marginal (nowadays, not so much one time!) space savings using plain text. I know some programs can read others. I never had any problem on Mac reading old Word files for example. I think a few very old ones became tricky. I donât even remember how I did it. Just with Pages mostly I think.
I have used LaTeX and donât bother keeping anything now other than the final pdfs. I have the same set up you do really. Anything that works for sharing, often docx, which Ulysses exports easily to, and Ulysses and DEVONthink 3 for anything else really. I did drop Ulysses but re subscribed: frankly I had over-thought the whole thing and if it ainât broke donât fix it.
I use Ulysses a lot. I take your point about the âflavorsâ and that is what made me reinstall Ulysses in fact. Familiarity and in fairness it is a really good and well maintained app. I drifted away though from my âruleâ about plain text. I find most things can be read by a lot of programs now and the savings in space I used to value plain text for are really marginal.
I am losing sight really of a lot of âunder the hoodâ stuff. Even things I used to know about quite well. I use Mellel too which is highly exportable from and a good app. Also, almost for old times sake really LaTeX. though I love that system and its design.
I was using Ulysses a lot as well but canceled my subscription a week or so ago. I like Ulysses but my biggest concern is the inability to bulk export individual sheets. This means that unless one uses an external folder (which also means you lose some of Ulyssesâ MD options) all of the sheets are exported into one single file/doc. This means that if one ever wants to move all of the sheets to something else, it is a sheet by sheet process.
Is this not a concern and if not, why?
You can batch export any group of Ulysses sheets to plain text by simply dragging them to an external folder. You have to add the external folder to Ulysses first. (You canât just drag into the Finder because youâll get unreadable .ulysses files.)
I cancelled Ulysses then resubscribed as I said. I donât use it in such a way that I ever need to export like that is the simple answer.
I didnât even know you couldnât do that: so thanks for the heads up about it really. If I ever do find myself needing that.
I just donât work that way, most of what I put on Ulysses either exports to another writing app or into DEVONthink 3 as a note pretty quickly or is just discarded. Most of the notes and stuff I take I collate by âhandâ as it were, extract from into another place or just delete. I leave them pile up and sometimes Houdah Spot finds something interesting in there I will admit.
I do have some notes in DEVONthink 3 that will only open in Ulysses and some that will open with any text editor: I donât know why that is or how I put them in there for that to happen. None of them are that important and if one day I canât open any of them, I will just suck it up!
Edit, I checked in your honor Bmosbacker and I think I moved some notes into DEVONthink 3 with the textbundle option ticked instead of âtextâ or whatever!
That is what I do with Ulysses, nothing important is there long enough to need batch move. Incidentally you seem a power user. I could never get Drafts to show in Finder; despite help from the developer and clicking all the correct options: I dropped it for that reason though at one time I liked it better than Ulysses. Any ideas about that?