Storing notes inside the file folder

Hey, I have tried many things over the months with J.D. But I really need to keep the notes that relate to the folder inside the file folder itself; there if very few, if any, notes that I need to take that directly link to my J.D files, but it’s still going to be useful.
Using a separate app or vault for the notes doesn’t make sense as there will be very few of them, and the extra friction of having notes and files in two distinct places makes it so that, I will only discover the notes for the files when I ACTUALLY search for notes relating to that file!

So, I need an app to read .md notes quickly to open them from the folder conveniently and to create them—but I want them stored inside the file folder and not in a separate location like with Obsidian. (nor SimpleNote, the recommended app)

I’m wondering if someone was in the same situation as me. Or, if not, has a recommendation on what to use to fulfil my needs?

Thanks a lot!

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Hey, I use iA writer for that purpose (there is a setting where it will ask where to save new files, instead of e.g. iCloud library). This way I can create and edit .md files stored in the file system. To search and open a .md file I often use spotlight or raycast command line and the file opens in iA (both previews the .md file also)

Is there areason you can’t just point Obsidian to the your JD folder as its vault?

I’ve variously used:

  • TextEdit (hardcore!)
  • Typora (pretty)
  • VSCode (l33t)
  • Other ‘it’s just a text editor’ editors that I can’t remember
  • Oh BBEdit (quick)

I’m curious to know why the ‘Keeping notes’ section doesn’t mention storing the notes under the ID directories and then, on the next section suggesst a more tedious double work solution for keeping track of decimal numbers (creating an index).

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Your timing is impeccable, John. :wink: I’m sitting here typing up a new page for ‘the index’, which will replace the current ‘tracking your numbers’ page. (The entire site is getting a refresh.)

I’m more convinced than ever that you need an index, but rather than using Airtable or a spreadsheet or whatever – all very ‘heavy’ solutions – what I do is just create a note per JD item.

I use Bear but any note app will work. So now your index is just the notes in your app and you search those to find the next available number.

The solution discussed above, saving individual notes in individual folders in your file system, doesn’t solve this. If anything it’s more cumbersome and less searchable. Now you have to create a folder, and put a note in it!

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Maybe I’m missing something - but it seems to me, if you have a JD directory structure without parallel apps’ files somewhere else - and all the files in the directory structure - why would you need an index? I’m thinking Obsidian here but just any file manager will do too.

So, I have - let’s say:

Directory: 20-29 Something
Subdirectory: 23 Something-something
Sub-subdirectory: 23.01 Whatever
Files inside, different kinds - spreadsheets, pictures
Sub-subdirectory: 23.02 Whatever next
Single Markdown note in it with my thoughts

Then I’m working - and need to save something as next item - be it whatever: picture, or note - in 23.

So - in Obsidian - as well as in any file manager - I immediately see that next free is 23.03 - I don’t
need any index for this.

Obsidian is just super easy - I create the note in it immediately, it’s very effort saving.

So why the index at all?

Does Obsidian create a folder when you create a note? I don’t use it, that’s interesting.

But yes, if you only use one (file) system, and the only place you save anything is that file system, then that file system can be the index.

The problem comes when you store something anywhere else. What about email? A notes app that doesn’t synchronise with your file system (I use Bear)? Files across multiple file systems (common at work)?

Then you must use an index.

Keen to flesh this out as I’m working on this page right now. Hit me with your thoughts!

Yes - this is good brainstorming.

So - Obsidian is really easy (you should check it out again):

You hit Ctrl-o for Open/search/create - on the phone (it has an awesome Android app, probably iphone too I’d guess) hit the open icon: and start typing. You’d go - if you don’t have the directory:

20-29 Something/23 Etc/23.01 Test file

It’ll create the directories and file.

If you have them - it’ll show you search results and you click it to open - very strong - so you’d just type 23.01 and click it. Or you just click it from the directroy structure window it shows you.

Now email:

So I guess you mean when you’d send a new email have it have the 23.03 tag and have it as a separate item in the JD system?

Well then, you’d have to create this directory to have as a reminder for the email. However, you’d also have to write it in the index file - same there - if you had it. However like this, you don’t have to reduplicate everything here etc in the index file - which you would if you had it.

Basically, I think, the directory structure is your index - with significantly less effort then keeping an index file.

This for me induces the question - why would you need more file structuring systems?

I’ve seen the discussion here on various Mac software that saves - as a design flaw in my opinion - to arbitrary locations. And then you’d need to track it, yes - because you couldn’t save in the JD directory tree - but there then, an index note saying then 23.03 in whatever app is the same as a directory still here, that can just be called appropriately, right? It seems it’s the same work as having an index file - but you don’t have to reduplicate the directory itself, holding all the files that can be stored there, in the index.

You might, outside of this, want a separate dir for all your photos, let’s say - that you might want to organize. But then it seems to me the above still applies - tracking numbers in the file - or in the main dir. I don’t seem to see the benefit of the index file.

At work I have two laptops: my company’s, and the government department’s that I work for.

I’m managing a migration-to-cloud project. My system is split across these two systems, and on each I might store a file in my own OneDrive (ugh), or on the shared Teams area (UGH!).

Or in my email! On either system.

I have stuff all over the place at work. An index is essential.


OK - I didn’t consider two computers, ala work etc.

OTOH - wouldn’t this be the case for two separate JD systems - one on the work PC, one for personal stuff?

Or - if work stuff would reside in some space, ala 20-29 then you wouldn’t need to index it on the home computer, no? Or is it because you need to work on work stuff also on the home computer, so need the index-structure and don’t have access to it at home?

My work situation is one single project/system, which I use across multiple domains/computers. Let’s say I work for consulting company BIGCO and the government department whose project we are executing is the Department of Fun, DOF.

The numbers are all intermixed. I have 26 Communications and that includes a weekly project status pack to my stakeholder that’s produced on my BIGCO laptop. It’s 26.01. Its master version is in the BIGCO Teams shared area, but then I email it out every week and get comments/queries by email so they live in BIGCO > Outlook > 26.01. (Yes, I create numbered folders in Outlook. For everything.)

Then I have another comms pack that contains sensitive DOF data — server names, IP addresses, the sort of thing we usually keep on the network — and it only exists in the DOF Teams area. It’s 26.06 and again might have an Outlook folder.

These are all real examples. Another: I have category 11 Accounts, requests, access that collects all those things. 11.01 might be the setting up of my DOF account, 11.02 is about my security pass at BIGCO, 11.03 is my request for MS Project, and so on. These items are scattered around my world but I don’t care! I have an index which tells me where they are.

How do I do that? Easy: every index item looks like this. (This is a real one, which I’ve obfuscated.)

I use Bear’s hashtags, which are hierarchical. You get a nice sidebar of clickable tags. The first line in each note is always the location of the thing. In this case, I submitted a request and the response came via email so that’s where that thing is.

Then I have some notes, which is me helping future me with keywords. I know at some point I’ll want to look up my ‘division’ or ‘branch’ again, and this request has them. I’ve already used this to help someone else raise a similar request.

With my index, I found my old request in ~5 seconds. Literally seconds. I open Bear, hit Cmd-Shift-F, type a couple of words, and there it is. People watch over my shoulder and literally exclaim out lout. “Wow … how did you do that?”

(And by the way, I could grab that screenshot without moving from my kitchen table where I’m having my morning tea because my index is synchronised to this iPad. From anywhere I can immediately tell you if I have a thing, and where it is. I make sure that the contents of the notes don’t contain anything sensitive.)

You could do this without an index, but in this situation I’d consider it essential. And look at how simple it is: it’s just a note. That note took me less than a minute to create. It’s not some heavy operation and I’ve already been paid back in the time that it took.

I think I’ll make the new website page for ‘the index’ really clear that if you have a single system in a single place then maybe you don’t need an index. I think that’s the confusion here. But as soon as it spreads out, which is inevitable in many situations, you need one. No question.

It might be a neat home/work split, but I also use an index at home for other reasons. Basically the same as the scenario above though: I have some things that are only files, some things that are only emails, and some things that are only notes. How would I track those without an index?


Yeah, thanks for this example - I think that makes it clear why it’s powerful to have the index, to bring everything together, and it can stay scattered as needed across systems and it’s not a problem.

My question about the screenshot:

What purpose does the tag serve? It’s basically the same as the PRO.AC so what further utility does it bring? In the index file I’d assume you have this PRO.AC.ID live under the PRO.AC so is the index needed for any searching or something?

Bear detects your tags and makes them selectable items in the sidebar. Selecting one filters your notes to that tag. It’s really nicely implemented.

If you put a / in the tag it nests them in folders. And they autocomplete with tab when typing them out.

This gives me a view of my categories in my sidebar. The index builds its own structure. Given how little time it takes to do, it’s worth it.

And just to be 100% clear, I have a bunch of systems — each of which has a PRO identifier — whose index is all in Bear, all thrown in there together. Each index entry is a note. There are many hundreds.

This is why Bear’s hierarchical tags, and the simplicity of the PRO.AC.ID notation, is nice. To find/show all BIGCO-DOF notes I can either filter by searching for BICGO-DOF., or just click the top-level tag in the sidebar.

(Also BIGCO-DOF is how I obfuscated this example, actually I use a letter and two numbers as outlined here. L43 in this case, which you may be able to figure out if you’re a spy. :wink: )

So do you not store the notes in the JD directory structure? I mean I guess it’s just visual representation what you’re talking about with Bear as in your screenshot - you can see a tree structure of the subdirectories - here achieved via tags, right?

That’s neat in Obsidian - you always see the tree in the structure:


And so on, so I guess there’s no need for the tags and filter - as I see the ACs etc as collabsible tree nodes, so the orientation is simple.

OTOH - if you say each index entry is a note - these might live on different systems - the index you have in just one file right? With the entries being links to these separate notes - now these would be in your JD structure on the local machine right? So - if you’d have - but maybe Bear doesn’t have this - a collapsible tree view of the JD structure - you wouldn’t need tags and filtering? Or am I still missing something?

Also - taking your email reference before, coupled with other systems:

So let’s say you sent some email in a BIGCO project on the work computer, which is relevant and you want to create an entry for it in the JD structure somewhere, with a number, with a reference to the work email - so that you know where it’s at.

Obviously you’d record it in the index file - but would you create a note for this entry, with the directory in the JD structure on your home machine, with the directory containing a note - and the note giving the description mentioned above - saying this is in the work BIGCO email?

Or how do you concretely do it?

I do not. Bear has its own internal system — you add a note and it’s just in Bear. This then synchronises via their cloud service to all of your Bear apps wherever you run it.

Basically the same as Apple Notes. You don’t ever see the file which is your note. It’s just in a managed database somewhere.

Yeah that’s right.

I have one note per JD entry, and in that note I say where the item is. I have this as the first line of the note so it’s really obvious. I just put:

  • Location: BIGCO laptop/email.

Another note may say ‘DOF laptop/email’, or ‘DOF/OneDrive’, or whatever.

So then do you really need the index file per se?

You can just have this right? You have the note for each entry and it’s automatically indexed when you list it in Bear - so then you see what the next number is.

This basically seems parallel to my thinking - of not needing the index as a file per se - on your setup you have the note for each entry with the appropriate tag and its location, pointing you to the system where it resides.

In my thinking I’d have it in the directory structure - there in the appropriate directories also have the individual Obsidian note files for each entry, giving me also the location - i.e. Work email etc?

It is an index - as you say - albeit not an index file, I was thinking you have one note file, or spreadsheet where you list everything.

As a side note - this way (as it basically seems to me the same, just with me it’s one main directory structure - with you it’s the note tag structure in one app) could entail many local separate directories - referenced via the main index.

I was thinking there are let’s say files you want to keep in a separate directories - but still have them in the JD structure - photos as an example.

I was thinking it might not be beneficial - in my case where I have the directory for all files - to also bring them into this and file it inside - as it would bloat it. Like this they could have a separate “Photo” dir and the subdirectories there - and these would then be indexed in the main index - with location “Photos” or whatever. This way you could have many file structures locally - where appropriate - yet all indexed centrally.

What do you think?

I don’t have a single ‘index file’.

My individual notes, as a collection, in Bear, are my index.