Issue #003: Your Second Brain = AI’s Interface

How to make your notes usable by AI, and by you

October 28, 2025

Welcome Back

Issues #001 and #002 explored philosophy and process. This issue is about the foundation: the infrastructure that makes everything else work.

Let’s talk about building a second brain that AI can actually navigate.

Claude Is My UI

Here’s something that might sound strange: I barely open Obsidian anymore.

I have thousands of markdown files. Daily notes going back years. Project docs, meeting notes, ideas, time tracking. Everything in plain markdown. But I don’t browse folders or search with Obsidian’s interface anymore.

Instead, I ask Claude.

“What did I work on last Tuesday?”

“Pull up the Tether spec from last week.”

“What tasks am I carrying over from yesterday?”

Claude navigates my vault better than I do. Finds connections I’ve forgotten. Surfaces tasks I would have missed. Analyzes patterns across weeks of notes.

The AI became the interface to my second brain.

The Before Times

Organized chaos. Notes scattered across apps. Tasks in my head or random places. I’d start my day trying to remember what I was supposed to do. End of day? Maybe I’d write down what I did.

Missing tasks. Losing context. Forgetting ideas. Spending an hour or more daily just organizing.

The problem wasn’t discipline. It was infrastructure.

The System

Now everything lives in markdown files. Plain text. No proprietary formats. No databases. Just files and folders that any tool can read.

Three commands run my day:

• /start-day → Planning. Pulls from calendar, inbox, and yesterday’s incomplete tasks. Writes everything into today’s daily note.

• /wrap-up-day → Reflection. Reviews git history across projects, reconciles tasks, updates ongoing work log, asks me insightful questions about what I did.

• /time → Tracking. Hours logged right in my vault. No external service needed.

Each command is a conversation, not a script. They save me that organizational hour daily. That’s 365+ hours a year.

But the real value isn’t time saved. It’s the insights.

The Aha Moment

The moment this clicked:

“You mentioned wanting to implement that webhook retry logic back on October 3rd. Should we tackle that now?”

I had completely forgotten. Buried in a daily note from three weeks ago. But because it was markdown, Claude found it. The AI revealed a pattern I couldn’t see: I’d been putting off that task for weeks.

That’s when I realized: AI isn’t just recall, it’s also reflection and discipline.

Your second brain becomes queryable. Analyzable. The AI sees across all your notes, finds patterns, surfaces forgotten context. You stop losing things because the AI never forgets where you put them.

Getting Started

Don’t overthink this. You don’t need my exact system. You need a system that works for you.

This prompt will walk you through designing your system step-by-step:

Help me design a second brain system built with Markdown files. I want this to be a deeply iterative process: ask me one question at a time, use my previous answers to inform your next, and gradually refine the structure, taxonomy, and workflows with me.

Your goal is to help me create a system that feels natural, flexible, and enhances my productivity. Focus on designing something we can collaborate on and evolve together and not just a one-time setup.

When asking questions, start broad (goals, priorities, use cases) and progressively move toward specifics (folders, file naming, metadata, linking, automation). Keep each step actionable.

Then actually have that conversation. Answer honestly. Let AI help you design something that fits your workflow, not mine.

Day one: Create a daily note. Write what you’re working on. Ask the AI to help you keep on top of it.

Day two: Reference yesterday. Add what you accomplished. Write what’s next. Check-in with AI at the start and end of your day.

The system grows organically. Eventually you’ll add project notes, meeting notes, ideas, templates. Structure emerges from use, not planning.

Your aha moment? When you ask AI to find something and it does. “What was I working on two weeks ago?” “What tasks have I been putting off?” When AI successfully navigates your notes to answer questions you couldn’t easily answer yourself, that’s when it clicks.

The Trap

Warning: don’t over-engineer this.

Obsidian has an incredible plugin ecosystem. Hundreds of ways to organize, tag, link, visualize. Like WordPress, a million ways to do the same thing.

I’ve lost entire days installing & tweaking plugins instead of using my notes. Building the perfect system instead of doing work. Complexity feels productive. But it’s just procrastination with prettier graphs.

Start minimal. Add tools only when solving a specific problem you actually have. Not problems you think you might have someday.

Your system should support your work, not become the work itself.

What This Enables

With this foundation, you can build on it. Slash commands like /start-day and /wrap-up-day work because structure exists. Time tracking without external tools works because it’s just markdown. AI pattern analysis works because everything is plain text.

I’m experimenting with tools that make markdown + AI collaboration seamless. More on that soon. There’s unexplored potential in better interfaces for AI-navigable knowledge systems.

Start simple. Build collaboratively with AI. Use it daily. Let the system grow.

Your second brain isn’t just for you anymore. It’s for you and your AI partner.

Cool Things From the Community

Comet by Perplexity

A browser that treats AI as a co-pilot, not a plugin. I’ve been testing both Comet and Atlas (the AI-native browser wars are heating up). Comet feels more feature-rich and stable right now. Get a free month of Pro with my link: pplx.ai/jkudish

Claude Code Status Line Customization

Customize your Claude Code status line to show context usage, current folder, and git status at a glance: github.com/sirmalloc/ccstatusline. Game-changer for managing your Claude code sessions.

Ian Nuttall’s Dev Changelogs

AI tool updates are exhausting to track. Ian aggregates changelog updates from Claude, Cursor, and other AI dev tools into a simple Telegram feed. No more hunting through release notes: x.com/iannuttall/status/1982097674019995847

Want to share your project here? Hit reply and tell me what you’re building. I love featuring interesting work from the community.

What I’m Shipping

Heads down on customer projects and internal tooling. The highlight? Built time tracking directly in my vault with the /time command.

No external service. No subscription. Just markdown and AI. Need reports? Ask Claude. It reads time tracking notes and gives insights.

This is the point: when your knowledge system is AI-navigable, you can build capabilities that normally require separate software.

Final Thoughts

That’s issue #003. The infrastructure matters. Build it collaboratively with AI. Start simple. Let it grow.

Your second brain is the foundation for everything else we’ll talk about in this newsletter.

One question for you: What would your AI see if it looked across all your notes today?

Keep shipping, Joey

P.S. If you build or improve your markdown system after reading this, hit reply. I want to hear what you created.

P.P.S. If you found this valuable, forward it to someone drowning in scattered notes. They can sign up at jkudish.com/newsletter.