Setting Up Your AI Vault - Agent Memory

You're setting up Claude Code as your General Agent for professional work. Your projects and rules aren't forgotten when you close the session. Claude reads your vault and starts with memory every time.

ai-vault

This setup separates memory and reasoning:

🗂 Memory – Your vault (notes, SOPs, tasks, rules)
🧠 Reasoning – Claude Code reads your vault and acts on it
📘 Skills – Teaching documents that make behavior predictable
🛠 MCP – Tool connectors for real-world actions (Gmail, Xero, etc.)

Think of it this way: Your vault is a Second Brain. Until now, it just stored knowledge. Skills give your Second Brain hands. Claude Code can now act on your knowledge, not just retrieve it.

The Problem

Most AI usage today is:

Chat-based — conversations that disappear
Ephemeral — no memory between sessions
Prompt-heavy — re-explaining context every time
Inconsistent — different results for same requests
Ungoverned — no rules, no accountability

Even advanced users copy-paste context, re-explain their rules, and lose knowledge over time.

The question: How do we make AI work like a trained professional, not a clever chat agent without context about your professional work?

The answer: Give it a filesystem. A folder of markdown files solves the memory limitation of chat-only models. Claude Code reads files before every conversation, so it thinks beyond a single session. Your vault becomes Claude's long-term memory.

The Core Insight

Separate memory from reasoning.

Role	Tool	What It Does
Memory	Obsidian Vault	Source of truth you curate (notes, rules, SOPs)
Reasoning	Claude Code	Reads memory, follows rules, produces work
Training	Skills	Explicit teaching — repeatable, reviewable, auditable

Mental model: Claude Code is a junior professional with access to your shared drive. Not autonomous. Not magical. Just capable and fast — and it follows your written instructions.

Key shift: Skills are teaching, not prompting. You write what the skill does, when to use it, how to do it, what not to do. This makes behavior predictable.

Why This Matters

Aspect	Without Vault	With Vault
Context per session	Zero	Full
Re-explaining needed	Every time	Never
Memory	None	Persistent
Aligned advice	Generic	Your goals
Pattern detection	Impossible	Automatic
Institutional knowledge	Lost	Accumulated

Claude Code without vault = Smart agent with amnesia

Claude Code with vault = Your personal operator who knows your goals, remembers your history, follows your rules, and builds on previous work.

One sentence: The vault turns Claude Code into a stateful partner that accumulates context, enforces your rules, and compounds knowledge over time.

Step 1: Install Obsidian

Download from obsidian.md

Step 2: Create Your Vault

Open Obsidian
Select "Create new vault"
Name your vault: skills-lab
Choose location: ~/projects/skills-lab
Click Create

Obsidian opens with an empty vault.

Step 3: Create AGENTS.md

This file contains all the governance rules for how Claude Code should operate in your vault.

In Obsidian, create a new note called AGENTS and paste:

# AGENTS - General Agent Governance

## Purpose

This vault is where I (human) and Claude Code (General Agent) work together on business workflows.

## Workspace Structure

skills-lab/
├── .claude/
│   ├── skills/        # Reusable expertise (SKILL.md format)
│   └── agents/        # Autonomous workers
├── references/        # Supporting documents
├── CLAUDE.md          # Project context (references this file)
└── AGENTS.md          # This file (governance)

## Governance Rules

1. **Skills go in `.claude/skills/{name}/SKILL.md`**
2. **Agents go in `.claude/agents/{name}.md`**
3. **Skills for guidance (2-4 decisions), agents for reasoning (5+)**
4. **Always read this file before operating**

## Active Projects

| Project | Series | Status |
|---------|--------|--------|
| Email Assistant | Email-1 to Email-7 | Starting |

Save the file. Now if you open vault folder you will notice an AGENTS.md file there. See direct markdown without any abstractions.

What Goes In Your Vault?

Your vault isn't just governance files. It's your professional memory:

Content Type	Example	How Claude Uses It
SOPs	`sops/client-onboarding.md`	Follows your documented process
Client Notes	`clients/acme-corp.md`	Knows context when writing emails
Task Lists	`tasks/this-week.md`	Prioritizes based on your priorities
Templates	`templates/weekly-report.md`	Uses your established formats
Meeting Notes	`meetings/2026-01-03-standup.md`	Remembers decisions and action items
Reference Docs	`references/pricing-tiers.md`	Gives accurate answers about your business

Start simple: Begin with just governance files (AGENTS.md, CLAUDE.md). Add knowledge as you work. Every note you add makes Claude smarter about your specific domain.

The accumulation effect: Each piece of knowledge you add compounds. Client notes help with emails. Meeting notes inform task priorities. SOPs ensure consistent execution. Over months, your vault becomes institutional knowledge that makes Claude increasingly effective.

Step 4: Create CLAUDE.md

This is the entry point Claude Code reads first. Create CLAUDE Note in the vault root:

# Skills Lab

This is my professional Claude Code workspace.

Read @AGENTS.md for governance rules, formats, and structure.

## Current Focus

- **Email-N series**: Building an Email Assistant

Save the file.

Personalizing Your CLAUDE.md

The example above is minimal. As you use your vault, personalize it to reflect how you work:

# Skills Lab

This is my professional Claude Code workspace.

Read @AGENTS.md for governance rules, formats, and structure.

## About Me

- **Role**: Marketing consultant for SaaS startups
- **Timezone**: PST (working hours 9am-5pm)
- **Communication style**: Direct, no fluff, bullet points over paragraphs

## My Preferences

- Use American English spelling
- When drafting emails, match the formality of the recipient
- Default to concise (3 paragraphs max) unless I ask for detail
- Always include next steps at the end of client communications

## Current Focus

- **Email-N series**: Building an Email Assistant
- **Priority client**: Acme Corp (see `clients/acme-corp.md`)

## What I'm NOT Working On

- Internal company communications (use templates from `templates/internal/`)
- Social media (handled separately)

Why this matters: Claude Code reads this file first. The more it knows about your preferences, role, and working style, the less you need to re-explain. Your CLAUDE.md becomes your professional profile that shapes every interaction.

Step 5: Open in Claude Code

Now test that Claude Code picks up your context.

cd ~/projects/skills-lab
claude

Test prompt 1:

What is this workspace and what governance rules should you follow?

Expected: Claude Code reads CLAUDE.md, follows the @AGENTS.md reference, and explains your workspace structure and governance rules.

If Claude Code responds with your vault-specific information, your General Agent is configured.

Step 6: Create the Folder Structure

Now that Claude Code understands your workspace, create the folders:

mkdir -p .claude/skills
mkdir -p .claude/agents
mkdir -p references

But wait — you can't see .claude in Obsidian. Folders starting with . are hidden by default.

Step 7: Enable Hidden Files in Obsidian

To see and edit .claude/skills/ directly in Obsidian, install the Show Hidden Files plugin.

Part A: Enable Hidden Folders

In Obsidian, click Settings (gear icon, bottom-left)
Click "Files and links"
Enable "Show hidden folders"

Part B: Install the Plugin

Go to github.com/polyipseity/obsidian-show-hidden-files/releases/tag/2.5.0
Download: main.js, manifest.json, styles.css
Open your vault folder in Finder/Explorer
Create: .obsidian/plugins/show-hidden-files/
Copy the 3 downloaded files into that folder
Create data.json in the same folder:

{
  "errorNoticeTimeout": 0,
  "language": "",
  "noticeTimeout": 5,
  "openChangelogOnUpdate": true,
  "showConfigurationFolder": true,
  "showHiddenFiles": true,
  "showingRules": [
    "+/",
    "-/\\.git(?:\\/|$)/u",
    "-/\\.venv(?:\\/|$)/u"
  ]
}

Part C: Enable the Plugin

Go to Settings → Community plugins
Click "Turn on community plugins"
Toggle "Show Hidden Files" ON
Restart Obsidian

Result: You can now see .claude/skills/ and .claude/agents/ in Obsidian's file explorer.

Where is MCP for Obsidian?

You might wonder: "Where is Obsidian MCP server to connect Claude Code to my vault?"

Answer: We're completing initial setup to start getting value with the simplest approach first. |

Claude Code can already:

Read your CLAUDE.md and AGENTS.md
Create files in .claude/skills/
Execute skills you define

We will setup MCP later as it adds value with actions Claude Code can't do natively.

Note: Obsidian MCP servers exist (like cyanheads/obsidian-mcp-server and mcp-obsidian) and add features beyond filesystem access:

MCP Feature	What It Does
Backlink discovery	Find all notes that link to a given note
Graph connections	Traverse note relationships via NetworkX graph
Tag/frontmatter search	Query notes by metadata, not just content
Vault structure	Get directory tree and connection patterns

(Optional) Git Version Control

If you want institutional memory — tracking every change to your skills and agents:

cd ~/projects/skills-lab
git init
git add .
git commit -m "Initialize skills-lab vault"

This is good practice but not required for the Email series.

Your Setup Complete

skills-lab/
├── .claude/
│   ├── skills/         ← Visible in Obsidian, ready for Email-1
│   └── agents/         ← Visible in Obsidian, ready for Email-4
├── .obsidian/
│   └── plugins/
│       └── show-hidden-files/
├── references/
├── AGENTS.md           ← Governance rules
└── CLAUDE.md           ← Entry point for Claude Code

What you have:

Obsidian = Human interface for reading/writing markdown
Claude Code = General Agent that operates in the same files
AGENTS.md = Single source of truth for governance
CLAUDE.md = Entry point that references AGENTS.md

Same files. Different interfaces. No translation layer.

Try With AI

Prompt 1: Verify Governance

Read my AGENTS.md and tell me: What are my governance rules? What format should skills use?

What you're practicing: Confirming Claude Code reads and follows your governance file.

Prompt 2: Create First Structure

Based on my AGENTS.md, create the folder structure I need for skills and agents if it doesn't exist.

What you're practicing: Having Claude Code execute based on your governance rules.

Prompt 3: Skill Preview

I'm about to create an email-drafter skill. Research and show me exactly what the file should look like and where it should go.

What you're practicing: Verifying Claude Code understands your skill conventions before you start Email-1.

The Problem​

The Core Insight​

Why This Matters​

Step 1: Install Obsidian​

Step 2: Create Your Vault​

Step 3: Create AGENTS.md​

What Goes In Your Vault?​

Step 4: Create CLAUDE.md​

Personalizing Your CLAUDE.md​

Step 5: Open in Claude Code​

Step 6: Create the Folder Structure​

Step 7: Enable Hidden Files in Obsidian​

Part A: Enable Hidden Folders​

Part B: Install the Plugin​

Part C: Enable the Plugin​

Where is MCP for Obsidian?​

(Optional) Git Version Control​

Your Setup Complete​

Try With AI​