@Dor, thank you so much for this relevant post. This post, written by @santi, is also relevant to this discussion.
I’ve been using (and marvelled at, not gonna lie) Obsidian for the last two weeks. One of the first thoughts I had was precisely using nested vaults, which I quickly dismissed while learning about the software in its Help Vault.
Having read your 9 tenets for using nested vaults, I totally agree with them and I believe they’re exactly what we need to use them correctly. Nested vaults should only be used when there is a specific reason for them. That excludes any situation where you can just have a separate vault to develop a set of notes, as you can just take them at the end of the process and integrate them into the main vault.
The only reason to use this is indeed to have some usefulness in compartmentalizing a set of notes even after developing them (so you can keep a separate graph and set of tags, backlinks, linked mentions, etc.) while also having the possibility of integrating references to those notes in another higher-level vault.
In my case, I started with the main vault where I tried to integrate various sets of notes. My main vault’s primary purpose is for me to keep track of my corpus of knowledge, so to speak, so it includes many different types of information.
To keep it organized, I use various strategies that are synergetic with each other:
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I use folders as a way of separating sets of notes by hard functionality (e.g. “Templates”, “Daily Notes”, “Fleeting Notes”, “Literature Notes”, “Permanent Notes”, “Concepts”, “Facts”, “References”, “[name of some project with various kinds of notes all related to it]”, etc).
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Do not underestimate the value of folders. These are handy for when your vault becomes too big and you can just move them around, extract a set of notes from the file explorer to a USB or another location, etc. This is important, and I believe those who use a flat hierarchy might lose a valuable hard organization of their notes which would facilitate the manipulation of the containers of their notes, i.e. their files.
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I use two different sets of tags meant to let me view notes according to some parameters. In each note, they are written at the foot of the note as such:
Tags: [Tags about a note’s functionality] | [Tags about the note’s contents]
The first kind is something like #Diary, #Definition or #Connection. It’s meant for me to be able to see notes with a specific functionality inside obsidian. But these tags don’t exclude the value of folder division by functionality, as you can see by the examples I gave above. The second kind of tags is about its contents, such as #Alchemy, #Friedrich Nietzsche, #Philosophy, #PKM, #Practicalities, etc.
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Indexes, MOCs, and all the kind of extra meta-notes are also useful in vast vaults, and you can even aggregate them in their own folder for easy access (without the need to mess with the names of the files themselves).
3.1 This also comes in handy for naming the notes. I use a similar strategy to @lizardmenfromspace, which he/she details here. This has not only the advantages he/she explores in that entry, but also lets me search specifically for a few things. For example, the format of the UID for my notes is generally “YYYY.MM.DD-HH.MM”, after which I write the note title. This lets me search for the notes I’ve written on a given month or a given year (if I search for “2020.10”, for example, I see the notes I’ve written during october, which is something you can’t do with tags, as they can’t be numbers), while guaranteeing redundancy and also letting me use the note title to link (if I write “[[note title”, I’m suggested the note by obsidian while I’m writing, even if I don’t use its UID). The only thing I’m missing is really the ability to use unlinked mentions, and I really hope obsidian devs address this issue. It would only need to recognise partial filenames of the files and use them as unlinked mentions, especially if this were restricted to excluding well-known sequences present therein such as UIDs, Luhmann IDs, etc.
3.2 I also think that the headers are a great way of organizing information that you can refer to specifically without the need of a new note (atomicity is important, but should not be the only strategy employed, especially when you have ideas you want to compartmentalize but are too interrelated to be separated from each other) and, with 0.9.5, blocks.
While all these strategies work well within a vault, what if I want to use a more streamlined process specifically for a concept I’m trying to develop? That’s where nested vaults are particularly handy. I can use a nested vault where I only use stripped-down note titles without the need to fit in my workflow mentioned above to develop the concept/project. I can have the benefits of a separate graph view, tags, mentions, etc, while also being able to integrate it in the main vault and make use of the extensive reference system between notes.
Don’t forget: the notes inside a nested vault are all accessible to the higher-level vault, including graph view, tags, etc, even those you create inside the nested vault.
I’ve tested notes with exactly the same name, one in the main vault and another in the nested vault, and everything worked fine. In the main vault, when I tried to link a text with the title of the notes inside the main vault, both appeared as suggestions, and if I chose the one in the nested vault, the [[title]] would be changed to [[folder\title]], so I needed to use the pipe. Besides that, everything works the same.
So, from what I gather, the only really hard rule of thumb is not to try to link, in any circumstance, to anything in another vault. But one question arises: is this even possible? I don’t think so: while you’re in the nested vault, you can’t even see what you have in the higher-level vaults, so how would you link to anything outside it?
One thing to be aware of, of course, is that if you create a tag in a nested vault, it will show up in the main one. If it is the same as another you have in the main, it will just show the note along with the other ones while you’re in the main vault.