Johnny Decimal Meets Obsidian: Two Systems in One Vault

In short: Johnny Decimal organises through folders, Steph Ango's vault system through metadata. Both are right — about different things. I use both side by side, with a dividing line that fits in one sentence.

The final part of my series, and the only one without a server. Earlier I sorted my files with Johnny Decimal — this is about which parts of that make any sense in a note-taking vault.

1. Two Systems, One Vault

My vault originally ran entirely on Johnny Decimal. Every note got a number, every number a place in the folder tree. That worked beautifully for contracts and tax documents — and not at all for notes.

The reason is in the nature of the things. A contract sits somewhere. A thought doesn't.

Alongside it there's Steph Ango's vault system, which takes the opposite position: avoid folders, make everything accessible through metadata and links. Every note carries a categories property, and queries produce the views you would otherwise build out of folders.

I spent a long time trying to decide between the two. The resolution was that the question was framed wrong.

2. The Actual Conflict: Folders Versus Metadata

Both systems solve the same problem — where do I find this again — by opposite means.

Johnny Decimal is folder-primary. The folder structure is the truth. A file has exactly one place, and that place has a number that never changes. The payoff is unambiguity: there are no two locations where something might be.

Steph's system is metadata-first. The storage location is irrelevant, the properties are what count. A note can appear in several views at once, because views come from queries rather than folders.

The conflict is real and can't be argued away. What dissolves it is realising that the two systems are talking about different kinds of objects.

An invoice exists as a file. It has a physical location, it gets archived, it has to be findable in ten years — without Obsidian too, in the file manager. For it, a fixed location is an advantage.

A thought about a book doesn't exist as a file but as a node in a network. It belongs to the book, to the topic, to the project that triggered it, and to the day I had it, all at once. Forcing it into a folder means throwing three of those four relationships away.

3. The Dividing Line

The rule it all comes down to fits in one sentence:

Only things that need a real storage location get a Johnny Decimal number. Everything that lives as a note runs on categories.

In practice that means:

	Johnny Decimal	Categories
What	contracts, applications, tax documents, project folders	journal, books, projects, meetings, courses, tools
Where	one fixed folder, mirrored in the file system	anywhere in the vault, location irrelevant
Accessed via	the number	queries over properties
Changes	never	constantly

The test I've adopted: would this thing exist without Obsidian? A PDF would. A note about a thought wouldn't.

Two consequences that follow from this, which I didn't see at first:

The numbered folders mirror real folders in the file system — in my case in the cloud storage where the documents actually live. Both sides are named identically. That's the real purpose: the note is an index into something that exists outside.

Numbered notes explicitly get no categories. Otherwise you'd have two competing ordering systems on the same object — and would have to decide, for every note, which one applies. Exactly the decision the hybrid is meant to abolish.

4. The Three-Level Linking Model

The number structure has three levels — area, category, ID. So you can navigate there from any note, each level links to the next:

note  ──jd──▶  ID note  ──category──▶  category note  ──area──▶  area note

A note about a project therefore carries a jd field pointing at the matching ID note. The ID note points to its category, the category to its area. Three queries produce the overviews from this: all notes for an ID, all IDs in a category, all categories in an area.

A simplification I only arrived at later: the ID notes themselves no longer carry a jd field. Their address is already in the filename — pointing them at themselves was a self-reference that explains nothing and broke the first query.

Sounds trivial. The mistake was setting the field mechanically everywhere instead of asking what it actually asserts: "this note belongs to that address." For the address itself, the assertion is empty.

5. Templates and Shared Vocabulary

Almost every note starts from a template. Templates carry two things: the categories assignment and the frontmatter fields you'll want to filter on later.

The rule that makes the biggest difference is taken from Steph and easy to underestimate:

Property names and values are reused across categories, not reinvented per category.

If genre is named the same and filled the same way for books, films and series, you can filter across categories. If every category invents its own vocabulary, you get the same fragmentation as with folders — only invisible.

That exact mistake happened to me when I built two new templates: both needed a status field, and without cross-checking, both would have used different values. I only caught it because I created them at the same time. Two weeks apart, I'd never have noticed.

Since then there's a shared status vocabulary for all categories: idea, evaluating, in-progress, done, deprecated.

Templates are composable, not exclusive. An author template and a person template both carry the same category and differ through an additional type field. That saves one category per role.

6. When a Date Belongs in the Filename

A small question with a surprisingly wrong first answer.

My first rule was: date in the filename for everything created via quick capture. Sounded plausible and was wrong.

The correct rule ties the date to the template, not to the capture method:

Journal notes → YYYY-MM-DD Title, with a time if known. Regardless of whether captured on the go via hotkey or added weeks later.
Meetings → also dated, but for a different reason: meeting titles repeat heavily. Without a date, three notes called "Sprint Planning" would be indistinguishable.
Everything else → title only. The creation date lives in the frontmatter, where it belongs.

The difference isn't cosmetic. The capture method is a property of the moment; the template is a property of the content. A rule tied to the method produces two differently named notes for the same content type — depending on how much of a hurry you happened to be in.

For evergreen notes the date is dropped on principle: they're meant to be timeless. A date in the title implies they're bound to a moment.

7. What I Got Wrong Along the Way

Renamed folders without checking the configuration

I renumbered the top-level folders and broke four configuration files in the process. Obsidian stores folder names in .obsidian/*.json as literal strings — for daily notes, templates and attachments. Renaming doesn't carry them along.

That's now a warning in my own conventions. Renaming folders in Obsidian is not a pure file operation.

Misused daily notes as a journal

Steph's rule: daily notes stay empty and exist only as a target for backlinks. In my vault, roughly 206 of them contained actual journal content — thoughts, notes, half-paragraphs, all stacked up chronologically.

Migrating them into roughly 260 individual notes was the single most laborious step of the whole rebuild, and I deliberately did not do it mechanically. A day with five thoughts doesn't automatically become five notes — some belong together, some are under two lines and belong nowhere.

Why bother: a thought inside a daily file can't be linked to. It has no title, no category, no relationships — it's just a paragraph attached to a date. Only as its own note does it become something you can point at.

Roughly 78 further notes consisted purely of a time entry. Those ended up in a single shared file — one line per day instead of one file per entry.

Two READMEs where one would have done

I kept the vault overview and the template reference separate. Both described rules, both were touched on every change, and regularly the answer was in whichever document I wasn't reading. Merged.

The same lesson as the map note in the files article: a document that holds two systems together is usually a symptom that the split is in the wrong place.

References and root not cleanly separated

Notes about people, places and tools sat in the main area among my own notes. The criterion that resolves this isn't length or importance:

Does the thing exist without me? Books, films, places, people, companies, tools → references. Journal, projects, meetings, my own thoughts → main area.

A book I'm reading belongs in references. My notes about the book belong in the main area. That sounds pedantic, but it's the difference between a catalogue and a thinking tool.

8. Where the Hybrid Hits Its Limits

The honest conclusion: there are two questions this system doesn't answer either.

Archiving. For the numbered folders I signal completion through a second date in the name. For notes there's no equivalent — a finished project note looks exactly like an ongoing one, as long as nobody maintains the status field. And status fields only get maintained as long as you remember to.

Multiple membership for files. The very problem the numbers were meant to solve comes back at the edges. Certain accounting documents could sit under two categories; I picked one and documented the decision. That isn't a solution, it's arbitrariness written down.

For notes the question doesn't arise — they may belong to any number of categories. That's the best evidence the dividing line is in the right place: where multiple membership is natural, metadata is the right tool. Where a thing must physically sit in one location, folders are.

Would I do it this way again? Yes — but I'd draw the dividing line first and then start. I did it the other way round: first forced everything into one system, then noticed it didn't fit half the material, then rebuilt. The rebuild was the work. The rule behind it was an afternoon of thinking.

Sources

stephango.com/vault — the metadata-first system, including kepano-obsidian as a starting point
How I use Obsidian — the underlying set of rules
johnnydecimal.com — the folder-primary counterpart
Obsidian Bases — the queries the category views are built from