Most notes are transient—written and forgotten. This system makes knowledge compound over time. Each note you write becomes part of an interconnected network where insights build upon each other, and every hour of thinking leaves something behind that makes future thinking easier.
This project manages multiple Obsidian vaults, each combining Johnny Decimal for structural organization with Zettelkasten for emergent meaning through connections. Vault maintenance is augmented by AI librarian agents.
Johnny Decimal provides predictable file location through hierarchical numbering. Every note has an unambiguous home. The structure eliminates the paralysis of infinite filing options and makes retrieval predictable.
- Systems: Top-level domains (LIFE, WORK, TECH).
- Areas: Major groupings within a system (1–F).
- Categories: Subdivisions within an area (1–F).
Zettelkasten creates emergent insight through explicit links between notes. Links carry meaning—they explain why connections exist.
- Atomic: Each note contains one atomic idea.
- Evergreen: Durable knowledge units designed for long-term value.
- Claim-titled: Titles express complete thoughts (e.g., "Writing forces sharper understanding") rather than labels ("Writing").
The hierarchy handles organization; the association handles insight. The AI Librarian bridges the gap by auditing link health, suggesting evergreen extractions, and scaffolding new systems.
Follow these steps to initialize your first vault:
-
Install Obsidian: Download from obsidian.md.
-
Initialize Vault: Open this repository folder as a vault in Obsidian.
-
Enable Core Plugins:
- Go to Settings → Core Plugins.
- Enable Bases (for dynamic indexes) and Backlinks (for Zettelkasten connections).
-
Create System Folders: Create a
_SYSfolder in your vault root to hold configuration files. -
Initialize Root Index: Create
00.00.mdin the root and add the following:# Vault Index
![[JDEX_00.00.base]]
-
Configure your first Base:
- Right-click
_SYS/→ New base → Name itJDEX_00.00. - Open the file, click the Filter icon, and add:
Property: file.name | Operator: ends with | Value: .00.00. - Set the view to Cards.
- Right-click
The Librarian Agent assists with organization and knowledge development. It proposes actions but never modifies files without explicit approval.
- Vault Scope: Agents work on one vault at a time. If context is missing, they will ask: "Which vault should I work with?"
- Pathing: All paths are relative to the selected vault (e.g.,
vaults/[name]/SYS/...). - Safety: Agents require per-vault confirmation for structural changes.
- Open your vault folder in VSCode.
- Ensure the GitHub Copilot extension is installed.
- Use the chat interface; it automatically detects definitions in
.github/agents/.
- Install Gemini CLI.
- Install the provided skill:
gemini skills install ./librarian-vault-manager.skill --scope workspace. - Reload your session with /skills reload.
| Command | Purpose |
|---|---|
| /construct-vault | Scaffolds a new system/structure through guided chat. |
| /daily-review | Identifies concepts mentioned 3+ times in journals for evergreen extraction. |
| /audit-links | Checks for orphaned notes and broken references. |
| /cleanup | Detects duplicates and naming inconsistencies. |
| /flashcards | Generates Anki-ready spaced repetition cards from your notes. |
Every evergreen note uses Area, Category, and ID (ACID) notation with a system prefix: SYS.AC.ID.
| Component | Description | Range |
|---|---|---|
| SYS | System code | 2-4 letters (e.g., LIFE) |
| A | Area | 1-F (Hexadecimal) |
| C | Category | 1-F (Hexadecimal) |
| ID | Unique ID | 01-FF (Hexadecimal) |
Example: LIFE.3A.07 (LIFE system, Area 3, Category A, ID 07).
- Hexadecimal: We use 0-F (16 slots) instead of 0-9 (10 slots) to maximize density.
- System Prefixes: Allows multiple separate JD systems within one vault.
- Automated Indexes: Using the Bases plugin to replace manual index maintenance.
- The
00area is reserved for system meta-information (indexes). SYS.00.00denotes the index file for a system.00.00in the vault root is the master index.
VAULT/
├── _SYS/
│ ├── JDEX_00.00.base
│ ├── JDEX_LIFE.base
│ └── TMPL/
│ └── Daily.md
├── LIFE/
│ ├── 00-IDX/
│ │ └── LIFE.00.00.md ← System index
│ ├── 10-Area Name/
│ │ └── 11-Category Name/
│ │ └── LIFE.11.01-Title.md
├── JRNL/
│ └── YYYY/MM/YYYY-MM-DD.md ← Daily notes
└── 00.00.md ← Root index
| Element | Pattern | Example |
|---|---|---|
| System folder | SYS/ | LIFE/ |
| Area folder | A0-Area Name/ | 10-Philosophy/ |
| Category folder | AC-Category Name/ | 11-Productivity/ |
| Note file | SYS.AC.ID-Title.md | LIFE.11.01-Title.md |
The system index file (SYS.00.00.md) acts as the entry point for a specific system. It links back to the master index and embeds the relevant Base file:
[[00.00]]
# LIFE System Index
Description of this system's purpose.
## Quick Navigation
![[JDEX_LIFE.base]]
Every evergreen note begins with a link to its system index to ground it in the hierarchy:
[[LIFE/00-IDX/LIFE.00.00]]
# Descriptive Claim Title
Content expressing a single atomic concept.
- Daily Capture: Record raw thoughts in
JRNL/YYYY/MM/YYYY-MM-DD.md. This is low-friction and transient. - Review & Extract: Run
/daily-review. When an idea matures, extract it to an evergreen note with a claim-based title and ACID ID. - Link & Connect: Place
[[links]]inline within sentences to explain context. - Audit: Weekly, run
/audit-linksand/cleanupto maintain the "garden."
For a consistent environment, use the provided docker-compose.yml.
- Set Permissions: Run
id -uandid -gand update thePUID/PGIDin docker-compose.yml. - Launch:
docker compose up -d. - Access: Navigate to https://localhost:3001.
Capture web content directly into your daily notes.
- Install the Obsidian Web Clipper browser extension.
- Docker Users: Run
./setup-obsidian-uri.shon your host.
- Install Anki and the AnkiConnect add-on (code: 2055492159).
- Install the Obsidian_to_Anki community plugin.