Codex + Obsidian Second Brain

A bilingual template for turning an Obsidian vault into a Codex-managed second brain.

This is not another note-taking layout. It is a small operating system for personal knowledge in the AI age: Obsidian keeps your knowledge local, durable, and linkable; Codex helps you ingest, connect, restructure, review, and reuse it as active context.

The goal is simple: stop treating AI as a chat box that forgets everything, and start giving it a living external knowledge base it can maintain with you.

中文说明

What This Gives You

• A clean Obsidian vault structure designed for human writing and AI maintenance.
• A project-level AGENTS.md that tells Codex how to work inside the vault.
• Source notes, long-term memory notes, project spaces, authored writing, and asset boundaries.
• Fictional sample notes that show the workflow without exposing private knowledge.
• English and Chinese vault templates in the same repository.

Repository Structure

.
├── en/       # English standalone Obsidian vault
└── zh-CN/    # Chinese standalone Obsidian vault

Each vault contains:

00 Inbox     # Raw intake and temporary captures
10 Projects  # Active work with concrete outcomes
20 Sources   # External source notes
30 Memory    # Long-term reusable knowledge nodes
40 Authored  # Original writing, reflections, drafts, and voice
90 Assets    # Attachments and local files

Quick Start

Clone the repository:

git clone https://github.com/thejaytang/codex-obsidian-second-brain.git

Choose a language vault:

cp -R codex-obsidian-second-brain/en ~/SecondBrain

Or:

cp -R codex-obsidian-second-brain/zh-CN ~/SecondBrain

Open ~/SecondBrain as an Obsidian vault.

Then open Codex at the vault root:

codex -C ~/SecondBrain

In Codex Desktop, use the vault folder as the workspace root. The important part is that Codex starts inside the vault root, where AGENTS.md lives.

How Codex Connects To An External Knowledge Base

Your external knowledge base does not need a database, plugin, or hosted service. It can be a local folder of Markdown files.

Codex can work with that folder when three things are true:

1. The vault folder is the workspace root.
2. AGENTS.md is placed at the vault root.
3. Your notes use stable structure, source metadata, and links.

AGENTS.md acts like persistent operating instructions. It tells Codex how to sort notes, when to preserve original writing, how to create memory notes, and what not to touch. Codex supports project instructions through AGENTS.md; see the official guide: https://developers.openai.com/codex/guides/agents-md.

This makes your vault more than storage. It becomes a working context layer that an AI agent can read, update, and use across tasks.

How To Use Codex With This Second Brain

Use Codex for intake:

Add this article to 20 Sources. Preserve the original link, summarize the core claims, and suggest memory notes worth creating.

Use Codex for distillation:

Review the recent source notes and create stable 30 Memory notes for ideas that are reusable across projects.

Use Codex for linking:

Find related notes for this project and add only meaningful backlinks. Do not create weak links.

Use Codex for project work:

Create a new project folder for this goal. Add a project overview, success criteria, open questions, and links to relevant source and memory notes.

Use Codex for writing:

Use my 40 Authored draft as the source of voice. Improve structure and clarity without replacing my position or tone.

Use Codex for review:

Run a weekly review. Identify unresolved inbox items, source notes that should become memory notes, stale projects, and writing drafts worth revisiting.

The Workflow

The system is built around a simple loop:

1. Capture everything useful in 00 Inbox.
2. Preserve external material in 20 Sources.
3. Distill durable ideas into 30 Memory.
4. Use 10 Projects for work with concrete outcomes.
5. Protect original thought in 40 Authored.
6. Keep files and media in 90 Assets.

The rule is: capture first, preserve sources second, distill later.

Why This Matters Now

AI changes the value of personal knowledge. A messy folder of notes is still a messy folder. A structured, source-aware, AI-readable vault becomes a personal context engine.

When your second brain is readable by an agent, it can do more than store memories. It can help you notice patterns, recover old ideas, build on previous work, and turn scattered inputs into a system that improves every time you use it.

That is the self-evolving move: your knowledge base becomes a place where you and AI compound judgment together.

Privacy

This repository is a sanitized template. It does not include private notes, real source collections, downloaded assets, workspace history, or third-party theme files.

Before publishing your own vault, always review staged files with:

git status --short
git diff --cached --stat

License

MIT