Obsidian Second Brain

What This Does

This automation helps you create and maintain a private Obsidian vault that Codex can work in directly.

Like the other self-bootstrapping automations in this library, there is no separate customization agent on this page. The second-brain agent customizes itself during setup: it asks about your goals, role, communication preferences, and source material before it creates the vault context and indexes.

There is also no single output example. The useful outputs depend on what you put in the vault. Common uses include:

• turning rough notes, PDFs, meeting notes, and exports into clean knowledge-base notes
• answering questions from your own stored context
• summarizing progress on a project or topic
• drafting meeting prep, reports, plans, or strategy notes
• keeping source indexes up to date so future sessions can find the right material
• learning your durable workflow preferences over time

Safety

This automation is designed for a private knowledge base. The starter skeleton is public, but your actual vault should be a new private GitHub repository.

Do not put private notes, source material, credentials, API keys, or conversation logs in a public fork. Codex can read and modify files in the vault, create commits, and push to the private repository if you ask it to. It should preserve original source material in raw_sources/, ask before destructive cleanup, and link synthesized notes back to the relevant source files.

Step-by-Step Setup

Step 1: Install and authenticate the tools

Before setup, install:

• GitHub CLI, then run gh auth login
• Codex CLI, then run codex and sign in
• Obsidian and the Obsidian CLI

You will also use the public second-brain Obsidian skeleton as the starting point.

Step 2: Create your private vault

Open Codex in the folder where you want the private vault to live.

You will see a message such as:

  Hooks need review
  3 hooks are new or changed.
  Hooks can run outside the sandbox after you trust them.

› 1. Review hooks
  2. Trust all and continue
  3. Continue without trusting (hooks won't run)

These hooks are part of the second brain to save your conversation histories (locally, not pushed) and learn your preferences. Review them if desired, then select Trust all and continue.

Then send this prompt:

I want to create my own private second-brain Obsidian vault from this public skeleton: https://github.com/kevins981/second-brain-obsidian

Please set it up for me.

Assumptions:

- GitHub CLI is installed and authenticated.
- Obsidian CLI is installed and available.

Step 3: Add your existing material

Put existing material into raw_sources/. You do not need to organize it first.

Good candidates include:

• an existing Obsidian vault
• Notion, Google Docs, or other exports
• PDFs and reports
• meeting notes
• rough notes and working documents
• old documents that may or may not still be current

Step 4: Initialize the vault

Open Codex from the root of your private vault, then send this prompt:

You are helping me initialize this Obsidian vault as a second-brain knowledge base.

The vault has two main areas:

- `raw_sources/`: original source files I already have. These may include rough notes, PDFs, reports, exports, meeting notes, or outdated documents.
- `knowledge_base/`: the clean knowledge base that you will help write and maintain over time. This may start empty.

Your job is to create three setup files and two index files:

Answer the agent's questions.

Now you can start using the Obsidian vault normally.

Common usage patterns

Add New Material

Put new files such as new meeting notes, design docs, into raw_sources/. You do not need to organize them first.

Then ask Codex:

Added some new files.

Note that because the vault is backed by git, the agent will automatically figure out which new files are added and ask you for clarification if needed. The ingest skill will also be automatically invoked.

Ask Questions

Ask questions directly. The agent will automatically gather context, memories, preferences before answering.

E.g.

What did we say about X?

Give me a summary of progress on project Y.

Draft New Work

Use the vault to draft new documents, plans, reports, meeting prep, or other artifacts.

Similarly, the agent automatically gathers relevant context before acting.

E.g.

Draft a meeting prep for [meeting/person/project].

Draft a report about [topic].

Turn these notes into a cleaner knowledge-base note.

Agent Behavior Customization

The agent automatically detects your preferences. You can also make this explicit by mentioning keywords such as remember that. E.g.

Don't ask me whether you should push doc changes to git. Just do it.

Agent will remember this preference.

Maintenance

The vault includes skills for recurring maintenance tasks.

housekeeping

Invoke this skill to keep the vault organized, e.g. update the file indices.

Use it every now and then. The agent will do housekeep as it works, but its still beneficial to do this once in a while.

organize

Use this skill when the folder layout has become messy and should be reorganized.

reflect

Use this to help the agent learn your preferences from recent conversations. The agent will keep track of your feedback automatically, but it can be helpful to run this every now and then.