I Used Claude Code to Johnny.Decimal-ify 7,500+ Notes

On January 6th, Obsidian CEO Steph Ango open-sourced obsidian-skills—teaching Claude Code how to edit Obsidian's three file formats: Markdown, Bases, and Canvas.

I tried it. Works great. But then I noticed a problem:

AI knows how to edit files. It doesn't know where files should go.

It's like hiring a secretary who types 200 WPM but doesn't know your filing system.

So I spent a weekend building a patch: obsidian-jdex-steward.

kepano Solved "How to Write." I Solved "Where to Put It."

kepano's three skills cover Obsidian's file formats:

Skill	What It Solves
Markdown	How to write frontmatter, links, callouts
Bases	How to build dynamic views (like Notion databases)
Canvas	How to draw knowledge graphs

These are "format capabilities"—AI learned Obsidian's syntax.

But the real challenge in knowledge management isn't format. It's structure:

Which folder should this note go in?
What other notes is it related to?
How do I find it among 7,000+ files?

You need an organizational methodology. I chose Johnny.Decimal.

Johnny.Decimal: A Numbering System for Humans and AI

Johnny.Decimal (JD) is a numbering scheme so simple it feels almost dumb:

Area (10-19, 20-29, ...)
  └── Category (21, 22, ...)
        └── ID (21.01, 21.02, ...)

My vault structure:

20-29 = Personal Knowledge
26 = Product Philosophy
26.01 = "Uncle J's Product Philosophy v3.0"

Why JD? Because it's extremely AI-friendly:

Pure numbers, no ambiguity — AI doesn't need to interpret "important" or "urgent"
Flat hierarchy — Three levels max. No getting lost.
Frontmatter-friendly — One jd: "26.01" field. Done.

Real World: 7,526 Files, Starting from 0%

My Obsidian vault has 7,526 Markdown files. 0% had JD numbering.

I ran my scanner:

python scripts/jdex_scan.py /path/to/vault

Output:

{
  "total_markdown": 7526,
  "with_jd": 0,
  "coverage": 0.0
}

0%. Expected.

Then I had Claude Code create the JD scaffold:

Global Index 00.00-JDex.md — Entry point to the entire vault
System Inbox 00.01-Inbox.md — Staging area for new notes
Category Indexes — One navigation page per category, dynamically generated with Dataview

Next, I added JD frontmatter to 6 core documents in my Product Philosophy folder:

---
jd: '26.01'
aliases: [Product Philosophy, Product Philosophy v3]
---

Thirty minutes later:

{
  "with_jd": 9,
  "coverage": 0.12
}

0.12% looks tiny. But those 9 files are my most-used core documents.

That's the point of progressive migration: don't aim for 100%. Cover high-frequency files first.

Design Philosophy: AI Executes, You Architect

My JDex Steward skill follows a few core principles:

1. Read-Only Scans, Explicit Approval

The scanner is always read-only. Any file changes require your approval. This isn't a technical limitation—it's a design choice. AI shouldn't reorganize your knowledge system without permission.

2. Progressive Migration, No Big Surgery

Phase 0: Scan — Look, don't touch
Phase 1: Scaffold — Create skeleton (indexes, templates)
Phase 2: New notes only — New notes get JD, old ones stay
Phase 3: Touch-and-migrate — Migrate old notes when you open them
Phase 4: Weekly cleanup — 15 minutes of maintenance per week

The goal isn't 100% coverage. It's "finding things got faster."

3. Preserve Old Names as Aliases

When migrating files, old filenames become aliases. Your muscle memory still works. Search doesn't break.

kepano + JDex = Complete AI Knowledge Management Stack

My Claude Code skill combo now looks like this:

Layer	Skill	Source
Format	Markdown, Bases, Canvas	kepano/obsidian-skills
Structure	JDex Steward	UncleJ-h/obsidian-jdex-steward

Format layer: "how to write." Structure layer: "where to put it."

Combined, AI can finally work like a real knowledge management assistant:

"Create a note about MCP protocol" → Uses correct frontmatter format
"Where should this note go?" → Suggests category and ID based on JD structure
"Generate an index for Product Philosophy" → Builds it with Dataview queries

Open Source

JDex Steward: github.com/UncleJ-h/obsidian-jdex-steward

MIT license. Use it however you want.

Installation:

cp -r obsidian-jdex-steward ~/.claude/skills/

Then tell Claude Code: "Scan my Obsidian vault for JD coverage."

Final Thoughts

In the AI era, the core challenge of knowledge management isn't "how to capture"—it's "how to find."

kepano's obsidian-skills taught AI Obsidian's syntax. My JDex Steward taught AI an organizational methodology.

Your vault might not need Johnny.Decimal—any system that helps you find things fast is a good system.

But if your vault has grown too large for search to save you, try this combo.