Claude Code Memory Setup

> 71.5x fewer tokens per session with Graphify + permanent memory across sessions with Obsidian Zettelkasten.

A complete setup to turn Claude Code into an agent with long-term memory and full codebase awareness — without wasting tokens re-reading files.

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Table of Contents

1. The Problem
2. The Solution (Overview)
3. Part 1 — Obsidian as Persistent Memory
4. Part 2 — Chat Import Pipeline
5. Part 3 — Graphify (Codebase Knowledge Graph)
6. Part 4 — Complete Workflow
7. Part 5 — Auto-Save Hook (Safety Net)
8. Real Results
9. Troubleshooting

The Problem

When working with Claude Code, two problems silently eat your tokens:

Problem 1 — Amnesia between sessions. Every time you open a new session, you have to re-explain your project: stack, past decisions, current bugs, what's left to do. Claude Code remembers nothing from the previous session.

Problem 2 — Codebase re-reading. Claude Code re-reads all your project files every session to understand the structure. A project with ~40 files burns ~20,000 tokens just for Claude to orient itself — before you even ask a question. If you run 10 sessions a day, that's 200,000 wasted tokens.

The Solution (Overview)

Two complementary systems, each solving a different problem:

Obsidian handles what was decided (declarative memory). Graphify handles how the code is structured (structural map). Together, Claude Code starts every session knowing everything — without re-reading anything.

Part 1 — Obsidian as Persistent Memory

Concept

A single, centralized Obsidian vault acts as Claude Code's "second brain." It stores decisions, context, progress, and knowledge for all your projects. Notes follow the Zettelkasten method: atomic (one idea per note), densely interlinked, with standardized metadata.

Claude Code accesses the vault through CLAUDE.md and custom skills.

Recommended Structure

~/vault/                              # SINGLE vault for all projects
├── CLAUDE.md                         # global instructions for Claude Code
├── permanent/                        # consolidated atomic notes
├── inbox/                            # raw capture (ideas, drafts)
├── fleeting/                         # quick temporary notes
├── templates/                        # note templates
├── logs/                             # global session logs
├── references/                       # reference material
├── my-project/                       # MOCs and notes for project X
│   ├── architecture/                 #   architecture, decisions, conventions
│   ├── pipeline/                     #   data flows, APIs
│   ├── data/                         #   schema, data model
│   ├── features/                     #   planned/implemented features
│   └── logs/                         #   project session logs
├── another-project/                  # MOCs and notes for project Y
│   └── ...
├── chats/                            # imported Claude chats
│   ├── code/                         #   from Claude Code
…

> Why a single vault? Having one vault per project fragments knowledge. With a single vault, a note about "Supabase Auth" links to both project A and B. The graph view reveals cross-project connections you didn't expect.

Step-by-Step Setup

Prerequisites:

• Claude Code installed and authenticated
• Obsidian installed (free: obsidian.md)

1. Create the vault:

Obsidian → "Create new vault" → choose a name and location.

2. Create the folder structure:

cd ~/vault  # adjust to your path
mkdir -p permanent inbox fleeting templates logs references
mkdir -p my-project/{architecture,pipeline,data,features,logs}

3. Create the CLAUDE.md:

This is the file Claude Code reads automatically. Create CLAUDE.md at the vault root:

# Vault — Instructions for Claude Code

## What is this vault
Centralized knowledge base for all projects.
Persistent memory across sessions.

## Project stacks
- Project X: React + Supabase
- Project Y: Python + FastAPI
(adapt to your projects)

## Zettelkasten Rules

### Note creation
- Use wikilinks: [[note-name]] (not markdown links)
- Mandatory YAML frontmatter on every note
- Filenames in kebab-case: `auth-flow.md`, not `Auth Flow.md`
- 1 concept per permanent note (atomicity)
…

4. Create a note template:

cat > templates/default-note.md << 'EOF'
---
title: {{title}}
tags: []
created: {{date}}
updated: {{date}}
status: draft
type: permanent
---

# {{title}}

## Context

## Details

## Related links
EOF