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How I Use Obsidian, Git, and Claude Code Web to Manage My Notes

How I Use Obsidian, Git, and Claude Code Web to Manage My Notes

TL;DR: Three tools, one coherent system โ€” Obsidian as the local knowledge substrate, Git as the version-controlled backbone, and Claude Code Web as the AI orchestrator that ties them together. This is a personal sovereignty setup that compounds over time.

The Problem With Most Note-Taking Systems

Most people's note-taking setup is one of two extremes: a cloud app that owns your data (Notion, Roam, Evernote) or a pile of flat markdown files with no intelligence behind them. The first trades ownership for convenience. The second trades convenience for nothing in return.

I wanted something different: local-first, version-controlled, and AI-augmented โ€” without locking myself into any single vendor. After a year of iteration, the combination that works is Obsidian + Git + Claude Code Web.

The Three-Layer Stack

Layer 1: Obsidian โ€” Your Local Knowledge Brain

Obsidian is a markdown editor that runs entirely on your machine. Every note is a plain .md file in a folder you own. No proprietary format, no account required, no data leaving your device unless you choose.

What makes Obsidian powerful is bidirectional linking. You link notes with [[wikilinks]], and Obsidian builds a graph of how your ideas connect. Over time, clusters emerge โ€” and those clusters tell you what you actually think about.

My vault structure:

00 Inbox/          โ† Capture everything here first
01 Projects/       โ† Active work with deadlines
02 Areas/          โ† Ongoing responsibilities (writing, health, finance)
03 Resources/      โ† Reference material
04 Archive/        โ† Completed or inactive
Atlas/             โ† Permanent notes, essays, distillations
Maps/              โ† Maps of Content (MOCs) โ€” semantic hubs
Sources/           โ† Script-generated digests and summaries
Templates/         โ† Reusable note structures

The key insight from LYT (Linking Your Thinking): don't organize prematurely. Dump into Inbox, process weekly, let structure emerge from connections rather than imposing it top-down.

Layer 2: Git โ€” Version Control for Your Mind

Your notes are code. Treat them that way.

A Git repository behind your Obsidian vault gives you:

Setup is minimal:

cd ~/your-obsidian-vault
git init
echo ".obsidian/workspace*" >> .gitignore   # skip UI state
git add .
git commit -m "initial vault snapshot"
git remote add origin git@github.com:you/vault.git
git push -u origin main

After that, a daily or weekly commit is enough. Some people automate this with a cron job or Obsidian's Git plugin. I run it manually โ€” the act of committing forces a quick review of what changed.

The discipline payoff: When you've been running a Git-backed vault for a year, you can git log --all --oneline your thinking. You can see when an idea first appeared, how it evolved, when you abandoned it, when you came back. That's a knowledge graph with a time dimension.

Layer 3: Claude Code Web โ€” The AI Orchestrator

This is where the system gets interesting. Claude Code Web (claude.ai/code) is a browser-based Claude interface that can read and write files in your vault directly.

Think of it as an intelligent co-author sitting alongside your notes. You give it access to your vault, and it can:

The key is that Claude Code Web has file system access โ€” it isn't just a chat window. It can read your vault, understand its structure, and make targeted edits. You're not copy-pasting; you're collaborating directly on the source files.

The Daily Workflow

Here's what the system looks like in practice:

Morning (5 minutes)

Open Claude Code Web. Run a daily curation command. It fetches AI papers from ArXiv, top Hacker News threads, relevant Reddit discussions, and synthesizes them into a single dated note in Sources/. One note, cross-domain, ready to read.

During the day (capture friction-free)

New idea โ†’ Inbox note with a timestamp. Article worth reading โ†’ [[bookmark]] it. Meeting notes โ†’ Template-generated with action items. The goal is zero friction on capture. Process later.

Evening (10 minutes, optional)

Ask Claude to find connections between today's new notes and existing Atlas notes. Sometimes it surfaces a link I'd missed. Sometimes it doesn't. Either way, the prompt forces me to think about where new information lives in my existing knowledge graph.

Weekly (30 minutes)

Why This Combination Works

Ownership. Every file is a .md file on your disk. Obsidian can be replaced with VS Code, iA Writer, or a terminal editor. Git can be replaced with any version control system. Claude Code Web can be replaced with any AI that has file access. The data never moves.

Compounding. Git gives you history. Obsidian gives you links. Claude Code Web reads both and synthesizes across them. Three months in, you have a system that knows more about your thinking than you consciously remember.

Low activation energy. The bottleneck in any knowledge system isn't capability โ€” it's friction. Capture is one keypress. Synthesis is one command. Publishing (to BearBlog, to WeChat, to Anki flashcards) is one more. The system gets out of your way.

Cross-domain signal. The highest-value insight almost always comes from connecting something in 03 Resources/technology/ to something in 02 Areas/writing/. A flat folder system buries these connections. A graph system with an AI scanning across domains surfaces them.

Common Pitfalls to Avoid

Over-organizing too early. If you find yourself spending more time on the structure than on the content, the structure is too heavy. Start with Inbox and Atlas only. Add folders when you have 200+ notes.

Treating AI output as final. Claude Code Web is a first-draft machine and a connection-finder. It is not a replacement for your judgment. Read every synthesis it generates. Edit aggressively. The value is in the speed of the first draft, not in accepting it verbatim.

Committing too rarely. Weekly commits are fine, but if you're doing serious writing, commit daily. You want granular history.

Neglecting the Inbox. Capture without processing is hoarding. A weekly Inbox review is non-negotiable. If you skip two weeks, the Inbox becomes a psychological burden and you stop capturing.

Getting Started

If you're starting from zero:

  1. Download Obsidian (free, obsidian.md). Create a vault in a local folder.
  2. Run git init in that folder. Add a .gitignore for .obsidian/workspace*.
  3. Create three folders: Inbox/, Atlas/, Sources/.
  4. Write 10 notes about things you've been thinking about lately. Link them with [[wikilinks]].
  5. Open Claude Code Web and point it at the vault folder.
  6. Ask it to find connections across your notes.

That's it. The system builds itself from there.

The Bigger Picture

This stack isn't really about note-taking. It's about information sovereignty โ€” owning your knowledge, owning its history, owning the intelligence applied to it.

Every note you write is a data point about how you think. Every link is a signal about what you believe connects. Every synthesis is a mirror held up to the patterns in your reasoning. The system that captures and amplifies those patterns has compounding returns โ€” the longer you run it, the more it knows about you, and the better it gets at augmenting your thinking.

Obsidian stores the thoughts. Git preserves them across time. Claude Code Web finds the patterns you'd miss on your own.

That's the system. Start simple. Run it consistently. Watch it compound.

Published from an Obsidian vault managed with Git and synthesized with Claude Code Web.

#claude #git #note-taking #obsidian #productivity