Second Brain: A Compounding Knowledge System

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.

Core Philosophy

1. Johnny Decimal (Structure)

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).

2. Zettelkasten (Connection)

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").

3. The Librarian (Automation)

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.

Quick Start

Follow these steps to initialize your first vault:

1. Install Obsidian: Download from obsidian.md.

2. Initialize Vault: Open this repository folder as a vault in Obsidian.

3. Enable Core Plugins:

   • Go to Settings → Core Plugins.
   • Enable Bases (for dynamic indexes) and Backlinks (for Zettelkasten connections).

4. Create System Folders: Create a _SYS folder in your vault root to hold configuration files.

5. Initialize Root Index: Create 00.00.md in the root and add the following:

   # Vault Index

   ![[JDEX_00.00.base]]

6. Configure your first Base:

   • Right-click _SYS/ → New base → Name it JDEX_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.

AI-Assisted Vault Maintenance

The Librarian system uses Gemini CLI subagents to assist with organization and knowledge development. These agents follow a Proposal-First mandate: they analyze and suggest actions but never modify files without explicit approval.

Core Skill: librarian-vault-manager

This is the foundational skill that provides the Johnny-Decimal and Zettelkasten "Constitution" to all agents. It ensures that every action respects ACID notation, atomicity, and structural integrity.

Specialized Subagents

For complex tasks, the Librarian delegates to specialized experts. You can invoke them directly using the @ syntax in Gemini CLI:

Agent	Purpose	Key Commands
@librarian	General coordination and ID lookups.	"Where should I put this note?", "Find ID for X"
@vault-auditor	Link health and graph connections.	"Audit links in the example vault", "Find orphans"
@vault-cleaner	Hygiene, duplicates, and renames.	"Clean up my inbox", "Check for duplicate notes"
@vault-scaffolder	Building new JD systems/areas.	"Create a new WORK system", "Scaffold Area 20"
@daily-reviewer	Journal-to-Evergreen crystallization.	"Review my daily notes from this week"
@vault-synthesizer	Knowledge compounding & bridge notes.	"Synthesize my notes on Topic X", "Any contradictions?"
@source-distiller	Processing articles/transcripts.	"Process this article into atomic notes"
@flashcard-generator	Spaced-repetition card creation.	"Generate flashcards for this note"

The Crystallization Principle

Following the "LLM Wiki" philosophy, the @librarian proactively identifies valuable insights during your CLI sessions and suggests "filing them back" into your vault. This ensures that transient chat context becomes durable, searchable knowledge.

System Architecture

ACID Notation

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).

Deviations From Canonical Johnny Decimal

• 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.

Standard Zeros

• The 00 area is reserved for system meta-information (indexes).
• SYS.00.00 denotes the index file for a system.
• 00.00 in the vault root is the master index.

Folder Structure

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

Naming Conventions

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

System Index Template

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]]

Note Template

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.

Workflow

1. Daily Capture: Record raw thoughts in JRNL/YYYY/MM/YYYY-MM-DD.md.
2. Review & Extract: Run @daily-reviewer. When an idea matures, extract it to an evergreen note using the transclusion/embed method (![[links]]) to maintain context without duplication.
3. Compound & Synthesize: Use @vault-synthesizer to find tensions between notes and create "Bridge Notes" that explore emergent themes.
4. Audit & Maintain: Regularly run @vault-auditor and @vault-cleaner to keep the "knowledge garden" healthy.

Advanced Deployment & Integration

Gemini CLI Setup

1. Install Gemini CLI.
2. Run the project setup script: ./.gemini/setup-environment.sh.
3. The specialized subagents in .gemini/agents/ will be automatically discovered.

Dockerized Obsidian

For a consistent environment, use the provided docker-compose.yml.

1. Set Permissions: Run id -u and id -g and update the PUID/PGID in docker-compose.yml.
2. Launch: docker compose up -d.
3. Access: Navigate to https://localhost:3001.

Web Clipper

Capture web content directly into your daily notes.

1. Install the Obsidian Web Clipper browser extension.
2. Docker Users: Run ./setup-obsidian-uri.sh on your host.

Anki Integration

1. Install Anki and the AnkiConnect add-on (code: 2055492159).
2. Install the Obsidian_to_Anki community plugin.

External Resources

• Johnny Decimal Official Guide
• Zettelkasten Method Overview
• Andy Matuschak’s Evergreen Notes