Your build workbook · 3 hours

Stop renting your AI's memory.

You have watched it happen… the session ends and the useful work disappears. Today you build a place for that work to live on your machine, under your control.

Build what I own

Why this comes first

Open a fresh agent session and ask what you decided yesterday. If you did not save the work somewhere it can reach, it starts cold. That is what we are fixing.

What is an agent?

An agent is AI with tools. It can inspect files and take actions. It still only knows what the current session can reach.

Why build the system first?

Asking an agent to work without durable context is like hiring help and hiding the project folder. You will keep paying to explain the same work.

You have already felt the reset.

You explained the project yesterday. Today the new session asks the same question… so you paste the same background again. That is dependency, not memory.

Graphify makes the connections visible. Obsidian keeps the result in local files you own. The agent can return to the work without making you rebuild the context from scratch.

Setup

Do not make the room wait on your setup

Now that you know why the foundation matters… get the machine ready before the live build.

Choose one path · Mac mini

Keep the whole system on one machine

The agent, Graphify, source files, exported vault, and Obsidian all live on the Mac mini. This is the simplest path because nothing has to cross machines.

If the Mac mini has no monitor, use Screen Sharing for Obsidian and SSH for terminal work.

Choose one path · VPS

Split the agent from the vault

The agent, Graphify, and source files run on the VPS. Obsidian stays on your Mac or laptop because a headless server cannot give you the desktop vault experience.

The exported vault moves back to your desktop with SCP, Git, or your approved sync method.

Required tool 01 · Mac mini path

Install the agent on the Mac mini

Open Terminal on the Mac mini. Install Claude Code with the current native installer, restart the shell, then make the command prove itself.

Mac mini · install agent

curl -fsSL https://claude.ai/install.sh | bash
export PATH="$HOME/.local/bin:$PATH"
claude --version

Check the official Claude Code setup page ↗

Do not continue until claude --version returns a version number on the Mac mini.

Required tool 01 · VPS path

Install the agent on an Ubuntu or Debian VPS

Your VPS provider gives you a username and server IP. Open Terminal on your local machine, connect over SSH, then install the server tools and agent.

Local machine · connect to VPS

ssh <username>@<server-ip>

VPS · install and verify

sudo apt update
sudo apt install -y curl git python3 python3-pip python3-venv pipx
curl -fsSL https://claude.ai/install.sh | bash
export PATH="$HOME/.local/bin:$PATH"

# Prove the server is ready
claude --version
python3 --version
python3 -m pip --version
git --version

VPS · prove file access

mkdir -p ~/ai-second-brain-demo/raw
cd ~/ai-second-brain-demo
printf "VPS ready\n" > setup-check.txt
ls -la setup-check.txt

You are ready when SSH reconnects, all four version commands work, and setup-check.txt exists inside the project folder.

Required tool 02

Install Python 3

Do not check the box because Python might be there. Prove it.

On a Mac

Open the official Python download page.
Download the current macOS installer.
Open the downloaded package and finish the installer.
Close Terminal. Open it again.

On Windows

Open the official Python download page.
Download the current Windows installer.
If you see “Add python.exe to PATH,” select it before installing.
Close PowerShell. Open it again.

Open the official Python download ↗

Verify Python · Mac

python3 --version
python3 -m pip --version

Verify Python · Windows

py --version
py -m pip --version

Both commands must return a version number. If they do not… Python is not ready.

Required tool 03

Install Obsidian

You do not need a finished vault yet. You need the app to open without drama. VPS users install Obsidian on their local Mac or laptop, not on the server.

On a Mac

Open the official Obsidian download page.
Download the macOS version.
Open the disk image and move Obsidian into Applications.
Launch Obsidian.

On Windows

Open the official Obsidian download page.
Download the Windows installer.
Run the installer and open Obsidian.
Stop when you reach the vault screen.

On Linux

Choose the package offered for your distribution on the official download page. Launch the app and stop at the vault screen.

Open the official Obsidian download ↗

Can you see the vault screen? Good. Obsidian is ready. Do not create the workshop vault yet.

VPS path · after export

Bring the exported vault back to your desktop

Graphify does the heavy work on the server. Obsidian opens the result locally. Replace the placeholders with the same SSH username, server IP, and export folder you used during the build.

Local machine · copy vault from VPS

# Run this on your local Mac or laptop, not inside the VPS
scp -r <username>@<server-ip>:~/ai-second-brain-demo/<exported-vault-folder> ~/Documents/

Open the copied folder in Obsidian. Click two linked notes. If both open, the server-to-desktop handoff worked.

Small is smart on the first run.

Use a clean test folder with no private material. Large PDFs can wait until you know the loop works.

Show me the pile you keep making AI reread

The information is already there, but the relationships are missing. Pick one folder you actually need to understand.

Open the folder you keep avoiding. Maybe it holds meeting notes. Maybe it is full of code or half-read PDFs. Do not clean it yet… look at what the folder view cannot tell you.

What kinds of files live in your pile?What would you ask if AI actually understood this folder?Which connections do you suspect already exist?

Make the machine show its work

Install Graphify and point it at a safe folder. Then make it prove what is connected.

Step 1

Install the graph tool

Package names move. Proof does not. Use the facilitator's verified command if the spelling below has changed.

Terminal · install

pip install Graphifi
Graphifi install

# If permissions fail on macOS
pipx install Graphifi

# Confirm your installation
graphify --help

Step 2

Prepare your test folder

Add 10–30 safe files to the raw folder. Enough to reveal structure… not enough to bury the first run.

Terminal · prepare

mkdir ai-second-brain-demo
cd ai-second-brain-demo
mkdir raw

Step 3

Run the graph

Read the report before you export. Otherwise you miss the part where the system proves it understood your files.

Agent · build graph

cd path/to/ai-second-brain-demo

# Inside your compatible AI coding agent
/graphify .

The receipts from your first run

Number of nodesNumber of edgesNumber of communitiesTop god nodeMost surprising connectionMost ambiguous connection

Read the receipts

The nanoGPT run found 73 nodes and 76 edges. It grouped them into 19 communities. The GPT class landed in the center… because the code put it there.

Extracted

Found directly in your source files.

Inferred

Reasoned from available evidence.

Ambiguous

Uncertain and waiting for your review.

Node

A concept, file, function, person, or idea.

Edge

A named relationship between two nodes.

Community

A cluster of closely related nodes.

God node

A central concept that many ideas connect through.

What did the graph prove that the folder view could not?

Put the memory somewhere you own

The export turns the map into local notes you can inspect and change. They stay after the AI session ends.

Terminal · export

graphify export Obsidian

01
Find the export folder
Wait for the export to finish and note its location.
02
Open folder as vault
Open Obsidian and select the exported folder.
03
Walk the graph
Open graph view, click your god node, and follow several links outward.

Which linked note should you review first, and why?

Give the agent access… not ownership

Install the Obsidian skills. Then make the agent write one useful note into your vault before this session disappears.

Verify the command before you trust it.

The source material shows inconsistent repository spelling. Your system should be built on what works today… not what a transcript remembered.

Agent · install skills

/plugin marketplace add Kapono/Obsidian skills
/plugin install install

Prompt · first linked summary

Read the graph report. Build one permanent Obsidian note that links every god node. Separate what the files prove from what the graph inferred. Put uncertainty in an Ambiguous section. If the evidence is not there, say so. Do not make the graph sound smarter than it is.

Do not accept vague output

The note must link the god nodes. It must separate evidence from inference. Anything uncertain gets marked Ambiguous.

What new insight did you write back into the vault?

A second brain dies without a loop

One graph is a demo. Rebuild after useful work… and the system becomes something you actually own.

01Capture

02Map

03Ask

04Write back

05Rebuild

06Repeat

Day 1Build small

Day 2Add sources

Day 3Ask better questions

Day 4Write back

Day 5Clean duplicates

Day 6Create one useful output

Day 7Review what changed

What useful output will you create from this graph in the next seven days?

Ownership looks like this

Do not stop at the first graph.

The files stay with you, and the graph stays inspectable. Useful work survives the chat… because you gave it somewhere to live.

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