Work through each module in order, or jump to any lesson as a reference. Every prompt is ready to copy.
Module 00 · Foundation20 min
Why Your Knowledge Is Leaking
Learning Goal
Understand the difference between how most people use AI (starting from scratch every time) and how this system works: building up knowledge that stays and grows.
Most people treat AI like a search engine. Ask a question, get an answer, close the tab, forget it. That is called RAG (Retrieval Augmented Generation). Every time you ask a question, the AI searches your files or the internet, grabs relevant pieces, and gives you an answer. Then it forgets everything and starts over the next time.
Andrej Karpathy, co-founder of OpenAI and the person who coined the term "vibe coding," recently described something better. Instead of asking Claude to find and synthesize documents every time, you have Claude pre-compile everything into a persistent, interlinked wiki once. From that point forward, every new piece of information you add gets woven into what already exists.
"Obsidian is the IDE. The LLM is the programmer. The wiki is the codebase."
Andrej Karpathy · OpenAI Co-Founder
RAG vs. the Second Brain
Attribute
Traditional RAG
Second Brain (This System)
Starting point each query
Raw documents, from scratch
Pre-built, synthesized wiki
Cross-document synthesis
Done over and over every time
Already done, baked into pages
Compounding value
None
Grows with every source you add
Contradiction handling
Ignored
Flagged and resolved during ingest
Adding a new source
Added to search index only
Updates 10 to 15 related pages
The Three Layers
Raw folder: Your original documents and exports. Read-only. The AI reads these but never changes them. Your source of truth.
Wiki folder: Structured pages the AI creates and maintains. Interlinked concept pages, an index, summaries. This is what you query.
Schema file: A rules document that tells the AI how to structure the wiki, handle new sources, and format pages. The constitution of your second brain.
The Compiler Analogy
Think of your raw files as ingredients. The AI is the chef. The wiki is the finished meal. Every time you add a new ingredient, the chef works it into the existing menu rather than starting a new kitchen from scratch. Karpathy found he didn't even need a vector database; the LLM is good at navigating a well-structured index file on its own.
Key Insight
One new source updates 10 to 15 existing wiki pages. The knowledge stays. Every future query reads from a richer base. That is the compounding effect.
Module 01 · Setup30 min
Recovering Your AI Memory
Learning Goal
Get your past AI conversation history exported and ready to feed into your second brain.
Most people have been using ChatGPT and Claude for over a year. That is hundreds of conversations: research sessions, business strategy, writing drafts, brainstorming, learning. It is all sitting locked inside those platforms doing nothing. Today you get it out.
Do This First
The ChatGPT export takes up to 24 hours and the download link expires after 24 hours. Request it before doing anything else in this module.
Path A: Bulk Export (Get Everything at Once)
Claude Export
Same-day delivery
Go to claude.ai and click your profile picture
Settings → Privacy and Data → Export Data
You receive a download link by email, usually within a few hours
Download the ZIP file; it contains all your conversations in JSON format
ChatGPT Export
24-hour wait, start now
Go to chat.openai.com → your profile → Settings → Data Controls → Export Data
Confirm the request; you'll get an email within 24 hours
Download immediately when it arrives; the link expires in 24 hours
You get a ZIP file containing conversations.json
Path B: Chrome Extensions (Export As You Go)
Use these for ongoing capture after the workshop. Install one now so it is ready.
Install the extension and open any Gemini conversation
Click the export icon that appears in the chat toolbar
Choose Markdown and save
Drop the file into /raw/inbox
What Is Worth Exporting
Business strategy sessions and planning conversations
Research on topics you care about professionally
Writing drafts and creative work you want to keep
Learning sessions on tools, frameworks, or industries
Key decisions you talked through with AI
Project scoping or problem-solving conversations
Tip
Start with 10 to 20 of your best conversations rather than dumping everything at once. The system is designed to grow incrementally; you can always add more.
Module 02 · Setup25 min
Building the Container
Learning Goal
Have Obsidian installed and a vault with the correct folder structure ready to receive your data.
Notion Users
Follow Module 03B instead for your workspace structure. You can skim this module to understand the folder concept; you will replicate it as a page hierarchy in Notion.
Step 1
Install Obsidian
Go to obsidian.md and download for your operating system. Free for personal use. After installing, open it and choose Create New Vault. Give it a name, something like second-brain. Pick a location you will remember. Everything is stored as plain .md files on your computer. No cloud lock-in. You always own your data.
Step 2
Create the Folder Structure
Right-click in Obsidian's left sidebar and create each of these folders:
folder structure
/your-vault
/raw ← dump exports, articles, PDFs here (AI reads, never edits)
/inbox ← drop new exports here (automation picks them up)
/processed← Claude moves files here after parsing
/wiki ← AI builds and maintains this
/concepts ← topic articles written by Claude
/people ← notes on people you work with or follow
/projects ← active and past project summaries
/decisions← key decisions and the reasoning behind them
/outputs ← Claude-generated summaries and reports
The raw folder is read-only. The AI reads from here but never edits anything in it. The wiki folder is where the AI writes. This separation is important; raw is your source of truth.
Step 3
Install Recommended Plugins
Go to Settings → Community Plugins → Browse to find and install. The table below is split by how you're using Obsidian — install what fits your edge, skip what doesn't.
Edge A · Note-takerEdge B · Second BrainBoth
Plugin
Who
What it does for you
Obsidian Web Clipper
Both
One-click save of any web article to /raw as clean Markdown. Also installs as a Chrome/Firefox extension. The fastest way to get external content into your vault.
Obsidian Git
Both
Auto-commits your vault to Git on a timer. Every change Claude makes is tracked and reversible. The safety net behind Module 10 — install this before you do anything else.
Graph View(built-in)
Both
Already in Obsidian. Click the graph icon in the left sidebar to see every note and every link visualized as a web. The benchmark from Module 07 (average in-degree) is measured here.
Dataview
Edge B
Query your vault like a spreadsheet. List all decisions made in Q4. Show every wiki page with no outgoing links. Filter projects by status. Becomes essential once your vault has 200+ notes.
Smart Connections
Edge B
Uses AI embeddings to surface related notes you haven't linked yet. A sidebar panel shows the most semantically similar pages to whatever you're currently reading. Finds connections Dataview misses.
QuickAdd
Edge B
Create custom macros that drop a new note into /raw/inbox in two keystrokes — with the right filename format and frontmatter pre-filled. The fastest desktop capture method before the automation picks it up.
Tag Wrangler
Edge B
Rename or merge a tag across your entire vault in one action. When Claude creates inconsistent tags during a compile run, this cleans them up without manual find-and-replace across hundreds of files.
Copilot
Edge B
Chat with your notes directly inside Obsidian using Claude, GPT-4, or a local model. Ask questions, get summaries, run the Digital Twin prompts from Module 09 without switching to another window.
Templater
Edge A
Far more powerful than Obsidian's built-in templates. Auto-inserts today's date, links to yesterday's note, prompts you for a title on creation. Keeps every new note consistently structured from the first keystroke.
Calendar
Edge A
Adds a calendar panel to the sidebar. Click any day to open that day's note. Dots appear on days with existing notes. Makes a daily notes habit significantly easier to maintain.
Periodic Notes
Edge A
Extends daily notes to weekly, monthly, and quarterly review templates. One click creates a structured weekly review that links to every daily note from that week. Pairs with Templater and Calendar.
Tasks
Edge A
Track tasks across every note in your vault with due dates, priorities, and filters. Create a single "Today" view that pulls tasks from meeting notes, project pages, and daily notes into one list.
Start with the "Both" plugins first. Add Edge A or Edge B plugins only once the core workflow is running — too many plugins at setup creates unnecessary complexity.
Step 4
Write Your Schema
Before you put any real data in, give Claude a one-page rulebook so it writes pages consistently from day one. Create a file called schema.md in the vault root and paste in the template below. Edit it to match your context — the more specific you make it, the better Claude's output will be.
schema.md template
# Vault Schema
## Page Formats
- **Concepts**: definition, why it matters, how I use it, related concepts
- **People**: role, how I know them, key interactions, open items
- **Projects**: goal, status, decisions made, next steps
- **Decisions**: context, options considered, choice made, outcome
## Naming Conventions
- Files: Title Case with spaces (e.g. "Content Strategy 2025")
- Do not use underscores or hyphens in wiki page names
- People pages: "First Last" (never a username or handle)
## Frontmatter Rules
Every page must include:
---
type: concept | person | project | decision
created: YYYY-MM-DD
sources: [list of source files]
---
## Contradiction Handling
If new information conflicts with what is already on a page:
- Do not silently overwrite — add a ## Conflicts section
- Note the conflicting source and date
- Flag for my review with: > ⚠️ Conflict: [description]
## Folder Rules
- Never write to /raw — that is read-only source truth
- New wiki pages go in /wiki under the appropriate subfolder
- Generated reports go in /outputs
- entity-map.md lives at vault root (configuration file)
Claude reads schema.md at the start of every compile, lint, and merge operation. Keep it updated as your conventions evolve.
Module 03A · Claude Code30 min
Claude Code + Local Vault
Learning Goal
Have Claude Code running inside your vault folder and ready to process files, run compile operations, and write to your second brain.
Who This Path Is For
People comfortable with a basic terminal window who want more control. Claude Code has direct file access, can process hundreds of documents in one operation, and can run batch jobs.
Step 1
Install Claude Code
Open your terminal and run:
bash
npm install -g @anthropic-ai/claude-code
If you get a permissions error on Mac, run sudo npm install -g @anthropic-ai/claude-code and enter your password when prompted.
Step 2
Navigate to Your Vault and Start Claude Code
bash
cd ~/Documents/second-brain # replace with your vault path
claude
Claude Code will start and display a prompt. It can now read and write every file in that folder.
Module 03B · Notion30 min
Notion + Claude MCP
Learning Goal
Have Claude connected to your Notion workspace and able to create, read, and update pages as your second brain.
Who This Path Is For
If you already use Notion daily and do not want to switch tools, this is your path. The second brain concept is identical; only the connection method changes.
Obsidian vs Notion at a Glance
Obsidian (Paths A & B)
Notion (Path C)
Setup difficulty
Moderate
Easy: just OAuth
Compile speed
Fast (direct file access)
Slower (one API call per page)
Data portability
Files you own locally
Cloud-hosted, export needed
Offline access
Yes
No
Best for
Power users, large bases
People already in Notion
Step 1
Connect Notion in Claude Desktop Settings
Open Claude Desktop → Settings → Connectors → find Notion → click Connect. Complete the OAuth flow in your browser. Approve access for your workspace. Restart Claude Desktop. No JSON files, no terminal, no API keys.
Step 2
Grant Page Access in Notion
This is the step most people miss. In Notion, open any top-level page → click the three-dot menu → Connections → select your Claude integration. All child pages are automatically included. Repeat for each top-level section you want Claude to access.
Claude can only see pages you explicitly share with it. You control exactly what your second brain can access.
Step 3
Test the Connection
Ask Claude Desktop: "What pages do you have access to in my Notion workspace?" Then try: "Create a new page called Second Brain Test with a one-paragraph summary of what a second brain is." If the page appears in Notion, you are connected.
Step 1
Add the Notion MCP Server to Claude Code
bash
claude mcp add --transport http notion "https://mcp.notion.com/mcp"
Complete the OAuth browser flow when prompted.
Step 2
Verify and Test
Run /mcp; you should see notion listed as a connected server. Then test with: "Search my Notion workspace for any pages related to business ideas and summarize what you find."
Notion Workspace Structure
structure
Second Brain (parent page, connect this to Claude)
/Raw Imports ← paste exported conversations here as sub-pages
/Wiki
/Concepts ← topic articles Claude will write and maintain
/People ← notes on people you reference
/Projects ← active and past project summaries
/Decisions ← key decisions and reasoning
/Outputs ← Claude-generated summaries and analyses
/Inbox ← quick capture, process weekly
Index (db) ← optional Notion database tracking all wiki entries
Module 04 · Workflow40 min
Seeding Your Brain
Learning Goal
Run your first compile operation and watch your wiki start to take shape from your real conversation history.
This is the moment where it all becomes real. You have your exports, your vault is set up, and Claude is connected. Now you feed it your history and watch it build.
Don't Overthink This
Drop everything you have and let Claude figure out what is worth organizing. You can always edit or remove things later. The goal right now is to get something in and see the system work.
Merging Multiple Sources?
If you are combining exports from Claude, ChatGPT, Slack, Fathom, or other tools, go to Module 06: Multi-Source Merging before this step. Processing sources separately creates duplicate pages and naming conflicts that are painful to untangle later. Module 06 takes you through entity mapping and conflict resolution first — then come back here to seed your vault with clean, unified source data.
Step 1
Drop Your Exports Into /raw
Put in whatever you have: your ChatGPT JSON export, your Claude ZIP export, individual Markdown exports from the Chrome extension, any notes or documents you want included. Notion users: paste into your /Raw Imports section as sub-pages.
Step 2
Run the Seed Prompt
Use the path you set up in Module 03A (Claude Code) or Module 03B (Notion). Paste this prompt and wait; this will take a few minutes depending on how much data you put in:
seed prompt
I have placed all my exported AI conversations in /raw.
These are real conversations I have had over the past [fill in time].
Please read through everything and build me a wiki that captures:
1. My professional interests and areas of expertise
2. Business ideas and projects I have worked on
3. Recurring themes in how I think and work
4. Key decisions I have made and the reasoning behind them
5. People, tools, and frameworks I reference frequently
Create organized wiki pages with backlinks between related ideas.
Write each page as a reference article, factual and clear.
Step 2.5
Connect every wiki page to a master index
Do this right after the seed run finishes, before you explore the vault. It wires all pages Claude created into one central index so nothing floats orphaned—every page links to the hub, the hub links out, and related pages link to each other in a graph LLMs can parse. Paste the prompt below in the same environment you used for the seed (Claude Code, Notion, or Desktop).
master index prompt
Create a master index that acts as the central node for all this content. Requirements: (1) the index links to every item, (2) every item links back to the index, (3) related items link to each other, (4) the structure is easy for LLMs to parse. The goal is a connected graph, not a floating table of contents.
Step 3
Explore What Was Built
Obsidian users: Open Graph View by clicking the graph icon in the left sidebar. Each dot is a page. Each line is a link Claude created.
Notion users: Open your Index database and switch to Gallery or Board view. Filter by topic tag to see clusters.
Step 4
Ask Your First Cross-Source Question
Try something that requires connecting ideas across multiple sources:
query prompt
Based on everything in my wiki, what are the 3 themes or opportunities
that appear most consistently across my thinking and work?
Synthesize across all relevant pages and cite which ones you are drawing from.
Notice the difference: you are asking Claude to reason across a knowledge base it already built, not search for something. The answer is synthesized from your actual history.
Step 5
Ask the Gaps Question
gaps prompt
What are the gaps in my wiki right now?
What knowledge is underrepresented that I should research and add?
Give me a prioritized list of 5 to 10 topics worth exploring next.
This is the self-improving loop. Your second brain tells you what it needs to grow. That list is your reading agenda.
Module 03C · Claude Desktop20 min
Claude Desktop + Local Vault
Learning Goal
Start a local Claude Code session from inside Claude Desktop, point it at your vault folder, and run compile operations without ever opening a terminal.
Who This Path Is For
Anyone who has Claude Desktop installed and wants to avoid the command line entirely. No config files, no MCP setup. Claude Desktop has Claude Code built in. You just point it at your folder and start working.
Step 1
Open Claude Desktop and Start a New Session
Open the Claude Desktop app. Look for the option to start a new Claude Code session. This is usually found in a sidebar, a "+" button, or under a menu labeled New Session or New Project.
Step 2
Select Local and Choose Your Vault Folder
When prompted for a session type, choose Local. You will then be asked to select a folder. Navigate to your Obsidian vault folder (the one you set up in Module 02) and select it. Claude now has read and write access to every file in that folder.
Make sure you select the root of your vault folder, not a subfolder inside it. Claude needs to see the full structure to create proper backlinks.
Step 3
If your exports are JSON, convert them to Markdown
The session is now live. If the files you brought in from ChatGPT or Claude are JSON (or otherwise not Markdown), ask Claude in this same Claude Code session to read those files and convert them to .md in the right place in your vault. That way the content shows up as normal notes you can open and link in Obsidian.
JSON → Markdown
Scan my vault for JSON files (including ChatGPT or Claude exports). Read each one and create equivalent Markdown files with clear titles and structure so they display as normal Obsidian notes. Put them alongside or under the same parent folder as the originals unless a different layout makes more sense—explain what you chose.
Why this step
Claude can read JSON, analyze it, and help you build wiki-style pages from it—but Obsidian is built for Markdown. Raw .json files will not appear as readable, linkable notes the way .md files do. If your exports are still JSON, prompt Claude to convert them to Markdown before you rely on browsing the vault in Obsidian.
Claude Desktop processes one context window at a time. If you have many large JSON files, split them into subfolders of 20 to 30 files and run the conversion prompt once per batch.
Module 05 · Workflow20 min
Keeping It Alive
Learning Goal
Have a simple, sustainable routine for keeping your second brain growing without it feeling like a chore.
Daily
2 minutes
Export any important AI conversation using the Chrome extension
Drop it into /raw/inbox
Do not organize it, just get it in
Weekly
15 minutes
Review what was added to the wiki this week
Clean up any pages that need refinement
Run a mini-compile if you dropped files manually: "Process any new files in /raw"
Monthly
30 minutes
Run the full Lint operation
Ask: "What has changed in my thinking this month?"
Review the graph view for new clusters
The Karpathy Flywheel
Every query you run, every output Claude generates: file it back into the wiki. Your explorations become permanent additions to your second brain. Over time, the wiki reflects not just what you have read, but how you think.
"I rarely touch the wiki directly. It's the domain of the LLM. I'm in charge of sourcing and asking the right questions."
Andrej Karpathy
The Lex Fridman Method
Lex Fridman feeds his second brain into voice mode and talks to it on long runs. He explains concepts out loud and asks the wiki what he is getting wrong or oversimplifying. This is the Feynman technique (learn by teaching) with a study partner who knows everything in your knowledge base.
Automating the Inbox with Claude Code Routines
The manual approach works. But if you want the system to run itself, Claude Code routines can do it for you.
The key insight: instead of tagging processed files with compiled: true and trusting that nothing gets missed, use physical folder separation. Files that are unread live in one place. Files that have been processed live in another. Claude never has to guess.
The Two-Folder Pattern
Physical separation beats metadata tagging
folder structure
/raw
/inbox ← you drop new exports here
/processed ← Claude moves files here after parsing
Everything in /raw/inbox is unread. Everything in /raw/processed has been handled. When you set up a daily Claude Code routine, it checks /raw/inbox at whatever time you choose. If files are there, it parses them, updates the wiki, and moves each file to /raw/processed. If the inbox is empty, it does nothing and exits. This solves the scale problem: even with thousands of files in /raw/processed, Claude only ever reads what's actually new.
Setting Up the Routine
Create a scheduled routine in your Claude Code project
In your Claude Code project, create a scheduled routine with this prompt and set it to run daily. From that point on, your only job is dropping files in /raw/inbox. The rest is automatic.
inbox routine prompt
Check /raw/inbox for any new files. If the folder is empty, exit.
For each file found:
1. Read the file and identify what type it is (Claude export, ChatGPT export,
meeting transcript, document)
2. Extract key information: decisions made, people mentioned, projects
discussed, tools referenced, ideas that recurred
3. Update or create the relevant wiki pages — do not overwrite existing
content, only add or refine
4. Add bidirectional links between new content and existing wiki pages
5. Move the processed file from /raw/inbox to /raw/processed
When done, print a summary: how many files processed, which wiki pages
were updated or created.
Updated Rhythm
Daily (2 min): Export new conversations → drop in /raw/inbox
Weekly (5 min): Review what was added to the wiki that week, clean up anything that needs refinement
Monthly (30 min): Run the Vault Graph Health audit (Module 07)
Both approaches work
The compiled: true frontmatter tag approach still works if you prefer it — but the two-folder pattern is simpler, more reliable, and easier to automate.
Closing the Loop: Filing Outputs Back Into the Wiki
Every time you run a query or analysis, Claude produces a response. Most people read it and move on. That response should go back into your second brain.
The logic is straightforward: if the output was worth generating, it is worth keeping. Query outputs represent your thinking at a specific point in time — they capture what your brain noticed, what questions it asked, and what patterns it found. Those are valuable data points, not disposable text.
The Pattern
Every output earns a permanent home
After any significant query or analysis, save the output to your wiki with this prompt:
file output prompt
Take the analysis you just produced and save it as a permanent wiki page.
Title it: [descriptive name] — [YYYY-MM-DD]
File it in: /wiki/[most relevant subfolder]
In the frontmatter add:
type: analysis
created: [today's date]
query: [one-sentence description of what I asked]
sources: [wiki pages or raw files you drew from]
Add [[wikilinks]] from this page to every concept, person, or project
it references. Also add a backlink in each of those pages pointing here.
Dated titles prevent accidental overwrites and let you see how your thinking evolves over time.
What Compounds Over Time
Cross-source queries: save as /wiki/queries/[topic]-[date].md
Decision reviews: save as /wiki/decisions/review-[date].md
Career framework output: already saved to /outputs — also link it from /wiki/self/career-analysis.md
Graph health reports: already saved to /outputs — link from a /wiki page tracking vault health over time
This is what Karpathy means by "the wiki reflects not just what you have read, but how you think." The wiki gets smarter every time you use it — but only if you file the outputs.
Module 06 · Deep Dive35 min
Multi-Source Merging
Learning Goal
Reconcile exports from Claude, ChatGPT, Slack, Fathom, and other tools into a single coherent vault without duplicates or naming conflicts.
The problem with a real second brain is that your knowledge doesn't come from one place. You have Claude exports, ChatGPT exports, meeting transcripts, a Slack workspace history, maybe a Notion database. Each source has its own format, its own naming conventions, and its own way of referring to the same people, projects, and ideas.
If you process them independently, you end up with three pages about the same client, five different spellings of the same person's name, and a wiki that contradicts itself. This module fixes that before it becomes a problem.
The Core Challenge: Entity Drift
The same entity appears differently across sources:
"Wags" (Slack) vs "Mike Wagner" (meeting note) vs "mike-wagner" (filename) — three references, one person
"Axe Cap" (internal shorthand) vs "Axe Capital" (formal) vs "the fund" (conversational) — three references, one company
"the Sandicot play" (chat) vs "Sandicot Municipal Bonds" (document) vs "the trade" (Slack) — three references, one event
When Claude processes each source separately, it creates separate wiki pages for each variation. Your graph fragments instead of compounds.
Step 1
Audit Your Sources Before Processing
Before dropping anything into /raw/inbox, run this prompt once with all your source folders visible. Read the report carefully — it shows you where conflicts will appear before they happen.
source audit prompt
I have exports from multiple sources that I'm about to merge into one vault.
Before processing anything, help me understand what I'm working with.
For each source folder I show you, identify:
- What format are the files in?
- What naming convention does this source use for people, projects, and dates?
- What are the 10 most frequently mentioned entities (people, companies, projects)?
- Are there any obvious naming conflicts with what's already in /wiki?
Sources to audit: [list your source folders here]
Do not create or modify any files. Output a source audit report only.
Step 2
Build an Entity Map
Once you know what each source calls things, build a master reconciliation map. This is a single file that tells Claude how to resolve naming conflicts across all sources. Review it carefully and correct anything wrong before the next step — everything that follows uses it.
entity map prompt
Based on the source audit, create a file called entity-map.md in the vault root.
Structure it as a simple lookup table:
## People
| Canonical Name | Also appears as |
|---|---|
| Michael Wagner | Wags, mike-wagner, M. Wagner |
| Taylor Mason | Taylor, TM, taylor-mason |
## Companies & Projects
| Canonical Name | Also appears as |
|---|---|
| Axe Capital | Axe Cap, the fund, AC |
## Events & Decisions
| Canonical Name | Also appears as |
|---|---|
| Sandicot Trade | the Sandicot play, the trade, the municipal deal |
Fill this in based on what you found in the source audit. Flag anything
you're unsure about with a ? so I can review it.
Step 3
Process Sources One at a Time
Process each source through /raw/inbox with entity-map.md active. Use this prompt every time. Process one source folder at a time — don't batch multiple sources in a single run, it makes conflicts harder to catch.
merge prompt
Process the files in /raw/inbox. Before creating any new wiki page,
check whether a page for that entity already exists — either by exact
name or by any alias listed in entity-map.md.
Rules:
- If a page exists: add new information to it, do not create a duplicate
- If an alias matches but the canonical name differs: use the canonical
name from entity-map.md, update the existing page
- If no match found: create a new page using the canonical name format
(Title Case, spaces not hyphens)
- Always add a sources: tag in frontmatter listing which export this
information came from
When done, report: pages updated, pages created, conflicts resolved,
anything flagged for manual review.
Step 4
Resolve What's Left
After all sources are processed, run one final pass to catch anything the automated steps missed. Review the proposals, approve the ones that are right, then apply them.
resolve prompt
Scan the wiki for potential duplicates and unresolved conflicts.
Look for:
1. Pages with very similar titles (e.g. "Axe Capital" and "Axe Capital Fund")
2. Pages that reference each other but aren't linked
3. Pages where the same fact appears with contradictory details
(different dates, different amounts, different outcomes)
4. Any entity in entity-map.md that still has multiple pages instead of one
For each issue found, propose a resolution: merge, link, correct, or flag
for manual review. Do not make changes yet — list everything first.
Source Tagging in Frontmatter
Every page created or updated during multi-source merging should carry a sources field in its frontmatter. This lets you trace any fact back to where it came from and filter your vault by source if you ever need to audit a specific export.
One page per person. One page per project. One page per major decision. Facts that contradict each other flagged and resolved. Source attribution on every page. Your vault stops being an archive and starts being a single coherent record of everything you've built.
Module 07 · Deep Dive45 min
Vault Graph Health
Learning Goal
Run a connectivity audit, fix orphaned notes, and build a living link graph — turning a vault that exists into one that actually thinks.
Most vaults have a hidden problem: the notes exist, but they don't connect. You can have 1,000 pages and still have 900 of them be islands — no one linking to them, nothing linking out. That's not a knowledge base. That's a filing cabinet.
This module is about graph health: measuring how connected your vault is, fixing what's broken, and building the infrastructure so new notes automatically find their place in the network.
Why Connectivity Matters
Obsidian's graph view is only as useful as the links that feed it. When you ask Claude a cross-source question, it can only synthesize what's connected. Orphaned notes are invisible to that synthesis. The goal is a vault where every note has at least 2–3 incoming links — meaning multiple other notes point to it, and it points back.
The Benchmark
A healthy vault has an average in-degree of 3–5. Most fresh vaults start around 0.4. Everything in this module closes that gap.
Step 1
Run the Connectivity Audit
Drop this prompt into Claude Code with your vault as the working directory. Read the report before doing anything else — the stats tell you where you stand.
audit prompt
Scan every .md file in this vault. Build a directed link graph — for each
note, track which notes it links to and which notes link to it. Then:
1. Calculate: total note-to-note edges, average in-degree, notes with
zero incoming links
2. Identify true orphans: notes with zero incoming AND zero outgoing links
(minimum 100 words — skip stubs)
3. Identify near-orphans: notes with fewer than 2 incoming links
4. For each orphan, find the top 5 most similar notes using keyword overlap
5. Write a report to /outputs/vault-graph-health.md with: overall stats, orphan
list, candidate connections with similarity scores
Do not modify any files yet. Report only.
Step 2
Apply High-Confidence Links
Some candidate connections will be obvious — high keyword overlap, clearly related topics. For those, Claude can write the links directly.
links prompt
Read /outputs/vault-graph-health.md. For any orphan with a candidate connection
scoring above 0.65 similarity:
- Add a [[wikilink]] to the candidate in both files (bidirectional)
- Append to an existing ## See Also section if one exists, or create one
at the end of the file
- Never duplicate a link that already exists
- Write a log of every change made
Flag any pairs scoring above 0.95 — those may be duplicate files worth
reviewing, not linking.
Step 3
Review the Rest
Connections scoring 0.35–0.65 need judgment. Claude prepares batches of 10 for you to review — each takes about 2 minutes.
review prompt
From /outputs/vault-graph-health.md, take the orphans with mid-range candidate
scores (0.35–0.65). Group them into batches of 10. For each batch, show me:
- The orphan note name and a 300-word preview
- Each candidate with shared terms highlighted
Ask me: should these be linked? If yes, what is the relationship?
Wait for my response before writing anything.
Step 4
Fix Source-Specific Issues
If your vault includes exports from Slack, Notion, or other tools, links often break because of naming convention mismatches — IDs instead of names, underscores instead of hyphens. Scan for broken links first, then fix.
fix prompt
Scan all .md files for wikilinks that don't resolve to any existing file.
List the top 20 unresolved targets by frequency.
For each one, determine:
- Is this a person name that exists as a file with a different naming format?
- Is this a channel ID or system identifier that maps to a readable filename?
- Is this a file that genuinely doesn't exist yet?
Propose fixes for the first two categories. Don't change anything yet —
list the proposed replacements first.
Review the proposals, then apply the ones that are correct.
What Success Looks Like
After running this module, your vault's average in-degree should be above 1.5, true orphans should be in single digits, and your graph view should show a connected web rather than isolated clusters. Run the audit again monthly as part of your maintenance rhythm.
Module 08 · Deep Dive45 min
Map What Compounds
Learning Goal
Run three career frameworks against your vault to discover which interests compound each other, which ones are draining you, and what professional season your notes suggest you're actually in.
This module is for people who feel pulled in multiple directions. Maybe you consult and write. Maybe you build products and do strategy. Maybe you collect skills the way others collect opinions. Most career advice tells you to pick a lane. This framework helps you find out which lanes are already feeding each other — using evidence from your own notes, not someone else's theory.
The prompt below runs three analytical frameworks against your vault simultaneously and saves the results as a Markdown report inside your second brain. Run it once your vault has real history in it — at least a few months of notes, projects, and conversations. The output is only as good as what's already there.
Who This Is For
Freelancers and consultants managing multiple service lines or skill sets
Career-changers trying to find their throughline across past roles
Multi-passionate people who aren't sure what to double down on
Anyone who feels spread thin and wants evidence-based clarity, not gut feel
Founders and operators whose interests have evolved as their business has
The Three Frameworks
Framework 1
The LINK Test
Scores every pair of your top interests on four criteria: Language crossover (do you describe one using the other's vocabulary?), Improvement (does growth in one make the other better?), Need (do you use tools or concepts from one to solve problems in the other?), and Cut (would removing one visibly hurt the other?). High-scoring pairs are your natural M-shapes — skills that reinforce each other. Low-scoring pairs are competing for your time without compounding.
Framework 2
The Sorting Hat
Assigns each interest a job based on evidence in your notes: Good At (track record of skill), Stability (generates or protects income), Optionality (opens future doors), or Restores (gives you energy). An interest can hold multiple jobs. Interests holding zero jobs are flagged as candidates to cut or park. This framework separates what you do from what it actually does for you.
Framework 3
The Vesting Schedule
Assesses where you are with each interest based on note frequency, recency, and depth of engagement: Actively Investing, Vested/Harvesting, Dormant, or Emerging. Each gets a recommendation: Invest More, Maintain, Harvest, Cut, or Watch. This is the reality check — it shows where your attention is actually going versus where you say it is.
How to Run It
The prompt first scans your vault and lists every interest, skill, domain, and role it finds — then pauses and asks you to confirm the list before scoring anything. Do not skip that confirmation step. You can add things Claude missed or remove things that are no longer relevant. The accuracy of all three frameworks depends on the quality of that starting list.
This Takes Time
This prompt does substantial work. Expect Claude to spend several minutes reading your vault before producing output. For large vaults (500+ notes), it may need to work in passes. The final report is saved as /outputs/interest-framework-analysis.md.
Run the Prompt
Paste this into Claude Code, Claude Desktop, or your Notion MCP session with your vault open. Fill in your vault directory path at the top if Claude cannot find it automatically.
interest framework prompt
Vault directory: [paste your vault path here, or Claude will scan automatically]
Weight notes from the last 90 days (verify today's date) more heavily.
You are analyzing my Obsidian vault to run three career/interest frameworks.
SETUP
1. Recursively scan the vault directory I give you (and any linked folders).
2. Parse all .md files, notes, project files, meeting transcripts, journal
entries, and any text-based documents.
3. Build a master list of every distinct interest, skill, domain, role,
project, or identity mentioned across my notes. Examples: job titles,
tools I use, hobbies, side projects, client work, reading topics, courses,
ideas I return to repeatedly.
FRAMEWORK 1: THE LINK TEST
For every pair of interests/domains (focus on the top 10-15 most frequent):
Score them on the LINK rubric:
L (Language): Do I ever describe one using the other's vocabulary?
I (Improve): Is there evidence that growth in one made the other better?
N (Need): Do I use tools/concepts from one to solve problems in the other?
C (Cut): Would removing one visibly hurt the other based on how I operate?
Score each 0-4. Output a table:
Interest A | Interest B | L | I | N | C | Total | Verdict
Verdict options: Competing / Adjacent / Compounding
Highlight the highest-scoring pairs. These are my natural M-shapes.
FRAMEWORK 2: THE SORTING HAT
For each interest/domain, analyze my notes to assign it a job:
GOOD AT: Evidence I have genuine skill or a track record here
STABILITY: This generates or protects income/security
OPTIONALITY: This opens future doors or increases my leverage
RESTORES: Evidence this gives me energy, joy, or recovery
An interest can hold multiple jobs.
Flag any interests that hold ZERO jobs. These are candidates to cut or park.
Output a table:
Interest | Good At | Stability | Optionality | Restores | Jobs Count | Recommendation
FRAMEWORK 3: THE VESTING SCHEDULE
For each interest that earned at least one job in Framework 2:
Assess its current stage based on note frequency, recency, and depth:
ACTIVELY INVESTING: Recent heavy engagement, still building capability
VESTED/HARVESTING: Solid baseline achieved, occasional use, not growing
DORMANT: Past interest, rarely mentioned, no recent activity
EMERGING: New interest, appearing more frequently in recent notes
Recommend: Invest More / Maintain / Harvest / Cut / Watch
Output a table:
Interest | Stage | Evidence | Recommendation
FINAL SYNTHESIS
1. Name my top 2-3 compounding stacks (interests that reinforce each other)
2. Identify my "golden thread" -- the invisible connector across my interests
3. Flag 2-3 interests I should consider cutting or parking based on the data
4. Suggest how my M-shape could be positioned professionally given the current
season my notes suggest I am in
OUTPUT FORMAT
Save a single Markdown report as /outputs/interest-framework-analysis.md.
Use clear headers for each framework.
Include an executive summary at the top (5-7 sentences max).
Be direct. If something is competing for my time without compounding, say so.
NOTES ON INTERPRETATION
- Weight recent notes (last 90 days) more heavily than older ones
- Repeated mentions across different contexts (meetings, journals, projects)
signal stronger investment than single mentions
- Look for language crossover: am I using marketing terms in engineering notes,
or systems thinking in creative work? That is evidence of compounding.
Start by listing all interests/domains you found. I will confirm or add to
the list before you run the frameworks.
Reading Your Results
Compounding stacks are interest pairs that scored 3 or higher on the LINK test. These are where you should direct most of your energy.
Zero-job interests from the Sorting Hat are not necessarily bad — they may be hobbies worth keeping. But if they are consuming professional time without any return, that is worth examining.
Dormant interests that still hold jobs like Stability or Optionality may be worth reactivating. Dormant interests with zero jobs can probably be officially parked.
The golden thread in the synthesis section is typically the most surprising output. It names the invisible connector across your work that others already see but you haven't named yet.
Module 09 · Apply35 min
Put Your Brain to Work
Learning Goal
Use your second brain as an active thinking partner — draft from your own history, battle-test ideas against your past self, wire it to an agent, and understand what private models unlock for sensitive knowledge.
Kezia has a workforce re-entry grant due Friday. Same foundation she's written for twice in the last three years — different program, same audience. Without her second brain she'd spend Tuesday rebuilding context. With it, one prompt surfaces her two strongest past applications, extracts the arguments reviewers funded, and flags what fell flat. By Wednesday morning she has a draft that's 60% finished. Not because the AI wrote it. Because she stopped starting from zero.
The moment the system pays for itself.
You've built the brain, maintained it, merged sources into it, and audited its connections. This module is the payoff: using it as an active collaborator in the work you already do. The prompts here are the ones people bookmark and keep open in a separate tab.
1 — Draft From Your History
Grants. RFPs. Strategy memos. Proposals. Performance reviews. Client briefs. Every document you have ever written is a data point about what works for your specific audience. Most people write each one as if the others don't exist. Your second brain changes that.
The pattern: give Claude the new brief, let it find your most relevant past work, extract what landed and what didn't, then hand you a foundation to build from — not a blank page.
One-Click Prompt
Find & Adapt Past Work
Paste this with your new brief filled in. Claude searches your vault for similar past documents, extracts the strongest elements, and assembles a starting foundation.
draft from history prompt
I need to write: [describe the document — type, audience, goal, length]
Search my vault for past work that is similar in any of these dimensions:
- Same document type (grant, proposal, memo, brief, report)
- Same audience or funder
- Same topic or domain
- Same stakes or context
For each relevant past document found:
1. Summarize what I argued and how I structured it
2. Note anything that worked well (funded, approved, well-received) based
on my notes
3. Note anything that didn't land, if there is evidence of that
4. Extract the 3–5 strongest sentences or passages I could adapt
Then give me a recommended structure for the new document based on what
has worked before. Do not write the document yet — give me the foundation
and wait for my confirmation before drafting.
2 — The Digital Twin
Your second brain is not just a record of what you know. It is a record of how you think — your past positions, decisions, frameworks, and the evidence you cited to support them. That makes it possible to do something no other tool can: run a new idea against your own intellectual history.
The digital twin isn't the AI pretending to be you. It's Claude reading your actual notes and arguing back using your own evidence. If you're about to make a decision you made before and regretted, it will find that. If you've shifted on something without noticing, it will name it. If your new idea is genuinely new, it will confirm that too.
One-Click Prompt
Pressure Test Against Past Me
Describe the idea or direction you want to test. Claude reads your vault and argues back using evidence from your own notes.
digital twin prompt
I am considering: [describe the idea, direction, or decision]
Before I commit to this, search my vault and do the following:
1. Find every time I have addressed a similar idea, direction, or decision
in my notes — even if the framing was different
2. Identify my past position: was I for it, against it, or ambivalent?
Cite the note and approximate date
3. Check for contradictions: does this new direction conflict with a
position I have held or a commitment I have made?
4. Look for relevant past outcomes: have I tried something adjacent before?
What happened?
5. Play devil's advocate using only evidence from my own notes — not
general reasoning, but things I have actually written or documented
End with: what does my own history suggest I should think carefully about
before moving forward?
3 — Wire It to an Agent
Once your wiki is well-structured and current, it becomes something more than a personal resource — it becomes the knowledge layer for an automated agent. The agent doesn't need to know everything you know. It just needs to be able to read your wiki on demand.
The use case that lands hardest for business owners: an onboarding agent that can answer any question a new team member asks, because every SOP, process, and decision rationale lives in the wiki. No handbook to maintain separately. No Slack threads to search. The agent reads the same source you do.
One-Click Prompt
Agent Knowledge Layer — System Prompt Template
Use this as the system prompt when configuring a Claude agent (or any agent) that should operate from your second brain. Fill in the role and constraints for your specific use case.
agent system prompt template
You are [role — e.g. "a process assistant for our team" / "a grant
research assistant" / "an onboarding guide"].
Your knowledge base is a second brain wiki located at [vault path].
Before answering any question, read the relevant wiki pages. The wiki
is the source of truth — prefer it over your training data whenever
the two conflict.
Wiki structure:
- /wiki/concepts — topic articles and frameworks
- /wiki/people — key contacts and context
- /wiki/projects — active and past project summaries
- /wiki/decisions — decisions made and reasoning
- schema.md — naming conventions and page format rules
Rules:
- Cite the wiki page you drew from when answering
- If the wiki does not contain an answer, say so explicitly —
do not invent information
- Do not modify or delete any wiki files unless explicitly instructed
- Flag anything that appears outdated or contradictory for human review
Your role: [describe the specific job — answer team process questions,
assist with grant applications, brief new clients, etc.]
Beyond Claude Agents
The pattern above works with any agent framework that accepts a system prompt and file access. Open-source options like Hermes, OpenCrawl, and nano-claw — as well as multi-agent orchestration tools — can all use your wiki as a knowledge layer using the same structure. The wiki becomes the stable, human-maintained ground truth that agents read from. You update the wiki; the agents stay current automatically.
4 — Private Models
Everything above assumes you're comfortable sending your vault content to a cloud API. For most people, that's fine. But some knowledge is different — proprietary research, client data, medical records, financial models, trade secrets, or anything governed by NDA.
Private models flip the architecture: instead of sending your data to a cloud model, you run the model locally on your own machine. Your second brain never leaves your hardware.
How It Works
Tools like Ollama let you run open-source models (Llama 3, Mistral, Phi) on a standard laptop or server. Your vault becomes the RAG (retrieval-augmented generation) knowledge base — the model reads your wiki files as context before answering. No API key. No data leaves your machine. The model is open-source; the knowledge is yours; the output is private.
The second brain you've built in this workshop is already structured for this. The /wiki folder, the schema.md, the clean naming conventions — these are exactly what a local RAG setup needs. The day you decide to go private, the vault is ready. The setup is a tooling change, not a content change.
This matters most for: researchers with unpublished data, consultants with client confidentiality obligations, healthcare and legal professionals, and founders who treat their strategy and IP as competitive advantage. The second brain becomes a private intelligence layer that no one else can access or train on.
Use Cases by Persona
One pattern, many applications. Here are six ways real people use a second brain as an active work tool — not just a filing system.
Student
Thesis & research writing
Second brain holds three years of research notes, papers read, and arguments drafted
Every new chapter starts with a query: "What have I already argued about this, and what's missing?"
The twin catches contradictions between chapters before the advisor does
Consultant
Proposals & client work
Three years of client deliverables, strategies, and outcome notes in the vault
New engagement starts with a search for the two most similar past projects
Time to first draft cut by more than half; quality goes up, not down
Business Owner
SOPs & team operations
Every process, policy, and decision rationale lives in the wiki
Agent answers new-hire questions by reading SOPs — no handbook to maintain separately
Onboarding time drops; process drift stops because the wiki is the single source
Grant Writer
Applications & funded history
Every past application, reviewer comment, and outcome is documented
New grant brief triggers a search: same funder, same population, similar ask
Successful language and structure carry forward; failed approaches get flagged
Entrepreneur
Strategy & idea validation
Business model, market notes, and past pivots all documented with reasoning
New direction gets pressure-tested against three years of actual decisions — not gut feel
Private model setup protects IP and competitive strategy from leaving the machine
Working Professional
Performance & career growth
Meeting notes, project outcomes, and feedback all feed the brain over time
Performance review season: one query surfaces every win and contribution from the year
Career framework (Module 08) runs against real history — not a LinkedIn summary
Module 10 · Safety25 min
Backup, Recovery & Troubleshooting
Learning Goal
Set up a complete version history for your vault so any mistake Claude makes is one command away from undone — and know exactly what to do in the three most common recovery scenarios.
Marcus runs a batch compile on 500 files on a Sunday afternoon. Claude is aggressive — it overwrites three project pages he cared about, creates 40 stub pages he doesn't want, and renames a folder in a way that breaks 60 wikilinks. He stares at the screen. Then he opens a terminal, runs two commands, and every change is gone. It took 45 seconds. He had set up Git version control two months earlier and completely forgotten about it until this exact moment.
The only insurance that actually pays out.
Most second brain disasters are recoverable. Almost all of them are preventable. This module gives you both: the safety net that makes recovery trivial, and the patterns that mean you rarely need it.
1 — Git as Your Undo Button
Every change Claude makes to your vault — every new page, every edit, every deletion — can be tracked as a Git commit. If something goes wrong, you roll back to the last known good state. If something goes partially wrong, you cherry-pick exactly what to restore.
This is the most important five minutes you will spend on your second brain setup. Do it once, forget about it, and let it run silently in the background.
Option A
Obsidian Git Plugin (Recommended)
In Obsidian go to Settings → Community Plugins → Browse, search for Obsidian Git, and install it. In the plugin settings:
Auto backup interval: set to 10–30 minutes. Every auto-save creates a commit silently.
Commit message: set to vault backup {{date}} so commits are timestamped.
Pull on startup: enable if you work across devices. The plugin handles push and pull automatically.
Obsidian Git requires Git to be installed on your machine. On Mac: git --version in Terminal — if Git isn't installed, macOS will prompt you to install it. On Windows: download Git for Windows and run the installer.
Option B
Terminal Setup (Claude Code Users)
If you're using Claude Code, you're already in a terminal. Run these three commands once from your vault folder:
Create a private repository on GitHub and push your vault to it. Your notes stay private (private repo, no indexing) and you now have an offsite backup. The Obsidian Git plugin handles this automatically once you set the remote. For Claude Code users: git remote add origin [your-repo-url] then git push -u origin main.
2 — The Safety Prompt Pattern
The best recovery is no recovery. Before any operation that touches a lot of files — a full compile, a lint pass, a multi-source merge, a graph health fix — run a dry-run prompt first. Claude describes exactly what it would do without touching anything. You read it, adjust if needed, then give the green light.
This takes 30 seconds and eliminates 90% of surprises.
One-Click Prompt
Dry-Run Safety Check
Paste this before any operation you're nervous about. Fill in the operation you're about to run. Claude tells you exactly what will change before it changes anything.
dry-run prompt
Before I run the following operation, I want a full preview of what
you would do. Do NOT make any changes yet.
Operation I am about to run: [paste the prompt you are planning to use]
For each action you would take, list:
1. What file would be affected (created, modified, renamed, or deleted)
2. What the change would be (new content, overwrite, append, rename to what)
3. Whether the change is reversible with git restore if I change my mind
Group by: files that would be created / files that would be modified /
files that would be deleted or renamed.
At the end, flag anything that looks risky — large overwrites, deletions,
or changes to files that are heavily linked.
Wait for my confirmation before proceeding.
3 — Recovery Playbook
Three scenarios, exact steps. All three assume you have Git set up — which is why Section 1 comes first.
Scenario A
Claude created pages you don't want
Claude compiled aggressively and created 30 stub pages, duplicate entries, or folders you didn't ask for.
bash — see what was created
git status # shows untracked (new) and modified files
git diff --stat # shows exactly what changed in tracked files
If you want to undo everything since the last commit:
bash — undo all changes
git restore . # revert all modified tracked files
git clean -fd # delete all untracked new files and folders
Run git status first so you know what clean -fd will delete. It is not reversible on untracked files.
Scenario B
Claude overwrote content you wanted to keep
A page you cared about was modified and important content was replaced or removed.
bash — inspect and restore one file
git diff "wiki/The Page Name.md" # see exactly what changed
git restore "wiki/The Page Name.md" # restore just that file
If the page was fine two commits ago:
bash — restore from a specific commit
git log --oneline -10 # find the commit you want
git restore --source=abc1234 "wiki/The Page Name.md"
Scenario C
Claude renamed files and broke your links
A rename operation changed filenames that other pages were linking to, leaving broken wikilinks throughout the vault.
bash — undo renames with revert
git log --oneline -5 # find the commit with the renames
git revert abc1234 # creates a new commit that undoes it
If you want to keep some renames and undo others, use the dry-run prompt from Section 2 to get a complete list of what was renamed, then restore individual files:
bash — rename back selectively
git mv "wiki/New Name.md" "wiki/Original Name.md"
git commit -m "revert rename: New Name back to Original Name"
4 — When Claude Gets Confused
As your vault grows past a few hundred notes, you will occasionally notice Claude starting to lose coherence mid-operation — creating pages that already exist, referencing files it hasn't read, or producing output that contradicts what you told it earlier. This is a context window problem, not a Claude problem. The vault has simply outgrown what fits in a single session.
Signs you've hit context limits
Creating duplicate pages despite entity-map.md existing. Referring to a file by an old name after you renamed it. Writing content that contradicts a page it just created 10 minutes ago. Missing obvious connections to wiki pages it processed earlier in the same session.
The Fix: Scope Down
Process in batches of 50 files, not the whole vault. Start a fresh Claude session for each batch.
Run Duplicate Detector first (Module 07) before any large merge or compile. Deduplicating before processing reduces context pressure significantly.
Use folder-scoped prompts: instead of "process everything in /raw", use "process only /raw/inbox/batch-01". Claude stays focused.
Commit between batches. Each clean batch gets its own commit so you have clear rollback points.
Read schema.md at the start of every fresh session. Remind Claude of your conventions before each new batch — it doesn't carry memory between sessions.
The maintenance rhythm protects you
If you're running the inbox automation from Module 05 — processing files in small daily batches as they arrive — you will rarely hit context limits. Problems happen when people let /raw accumulate for months and then try to process everything at once. Small and regular beats big and occasional every time.
Bonus · Experimental20 min
Capture Anywhere
What This Is
An experimental extension for people who want to feed their second brain from their phone and voice — without touching a computer. Workflows here are real but require more setup than the core modules. Results will vary based on your devices and sync setup.
Experimental Content
The core workshop (Modules 00–10) works reliably on any computer. This bonus module explores mobile and voice capture workflows that are genuinely useful but more setup-dependent. Sync behavior in particular varies across devices, operating systems, and vault sizes. Treat this as a starting point for your own experimentation, not a guaranteed path.
The best insight you have all week might happen in the car, on a run, or in the middle of a conversation. If it doesn't get captured in the next 30 seconds, it is probably gone. This module closes that gap — building a path from a phone tap or voice memo directly into your vault without friction, and without waiting until you're back at a desk.
The key connection: everything you capture on mobile eventually lands in /raw/inbox, where the automation you built in Module 05 picks it up and integrates it. You do the capturing. The pipeline does the rest.
1 — Sync Your Vault to Mobile
Before you can capture to your vault from a phone, your vault needs to be on your phone. Three options, honest tradeoffs:
Option A
iCloud (Mac + iPhone only, simplest)
Store your vault folder inside ~/Documents or ~/Library/Mobile Documents on Mac and enable iCloud Drive sync. On iPhone, install Obsidian from the App Store and open the same vault location. Changes sync automatically through iCloud.
Works well for: Mac + iPhone users with a vault under ~5,000 files. Watch for: iCloud sync can be slow on first setup for large vaults. Keep your vault out of iCloud if you work with sensitive files you don't want in Apple's cloud.
Option B
Obsidian Sync (cross-platform, paid)
Obsidian's native sync service ($4/month) works on Mac, Windows, Linux, iOS, and Android. End-to-end encrypted. Open Obsidian on desktop → Settings → Sync → Create new remote vault. Then install Obsidian on mobile and connect the same remote vault.
Works well for: Anyone who uses both iPhone and Android, or Windows + mobile. Fastest sync of the three options. Watch for: Sync conflicts are possible if you edit the same file on two devices before they sync. The conflict resolution UI is workable but annoying.
Option C
Dropbox or Google Drive (experimental)
Store your vault in a Dropbox or Google Drive folder. Both sync to mobile via their respective apps. On iPhone/Android, use the Obsidian app and point it at the synced folder location.
Works well for: People already paying for Dropbox or Google Drive who don't want another subscription. Watch for: This is the least reliable option. Dropbox/Drive are not designed for vaults with thousands of small files and can be slow or inconsistent. Test with a small vault first. If you hit sync errors, switch to Option A or B.
2 — One-Tap Mobile Capture
Once your vault is on your phone, set up a shortcut so creating a new inbox note takes one tap from your home screen — not three taps, a folder navigation, and a filename decision.
Setup
Obsidian mobile quick-capture shortcut
In the Obsidian mobile app:
1. Go to Settings → Core Plugins → Templates and enable it. Set the template folder to a folder called /raw/inbox.
2. Create a template file called quick-note.md with this content:
3. Add a toolbar shortcut to Create new note from template using quick-note. On iOS, this shortcut can also be added to your home screen as a widget via the Obsidian widget.
From then on: tap the shortcut, type or dictate, done. The note lands in /raw/inbox and the daily automation picks it up that night.
Name quick-capture files with the date prefix: 2025-06-12-car-idea.md. Datestamped filenames make it easy to batch-review captures before the automation runs.
3 — Voice to Vault
Voice capture is faster than typing for longer thoughts — a 2-minute voice memo can capture more context than 5 minutes of typing. The challenge is that voice notes are messy: filler words, incomplete sentences, no structure. The prompt in this section handles that.
The Pattern
Record → Transcribe → Drop → Process
Record: Use your phone's native Voice Memos app (iPhone) or Recorder app (Android). Any voice memo app works — the output is an audio file or auto-transcription.
Transcribe: On iPhone, Voice Memos auto-transcribes if you're on iOS 16+. Tap the memo, tap the transcription icon. Copy the text. On Android, use Google Recorder — also auto-transcribes and lets you copy text directly.
Drop: Create a new note in /raw/inbox (using the quick-capture shortcut above), paste the transcript, save.
Process: That night, the inbox automation from Module 05 reads the transcript, extracts the key information, updates the wiki, and moves the file to /raw/processed. You don't touch it again.
One-Click Prompt
Capture: Raw Note Processor
Use this when you have a messy mobile capture or voice transcript that's too rough for the standard inbox automation to handle cleanly. Paste it here first, get structured output, then drop the structured version into the wiki.
raw note processor prompt
I have a raw capture — a voice transcript or quick mobile note. It is
messy, incomplete, and unformatted. Do not clean up or polish it.
Instead, extract what is worth keeping.
Raw capture:
[paste your voice transcript or mobile note here]
Extract:
1. The core idea or insight in one clear sentence
2. Any decisions made or conclusions reached
3. Any people, projects, or topics mentioned that have wiki pages
4. Any action items or follow-ups implied
5. Any questions that need answering
Then: is this worth a new wiki page, an addition to an existing page,
or just a note filed in /wiki/journal? Recommend one and explain why
in one sentence.
Do not write the wiki page yet — give me the extraction first.
4 — The Full Loop
When all the pieces are connected, this is what the daily flow looks like for someone using mobile capture:
Morning walk: voice memo with three ideas → transcribes automatically → one tap to drop transcript into /raw/inbox
Client call: quick note in Obsidian mobile during the debrief → one tap, 30 seconds
Evening: inbox automation runs → voice transcripts and quick notes extracted, structured, added to the wiki → files moved to /raw/processed
Next morning: wiki updated with everything from yesterday without touching a computer
The second brain captures when you're away from the desk and processes while you sleep. The only part that requires you is the initial drop into /raw/inbox — and that takes less than 30 seconds.
Start smaller than you think
Don't try to set up sync, quick-capture shortcuts, voice memos, and automation all in one session. Pick one entry point — probably the quick-capture shortcut — and use it for a week before adding anything else. The goal is a habit, not a system.
Prompt Library
Every prompt, ready to copy.
These are the core operations that run your second brain. Save them, use them, adapt them.
CompileSeed Prompt: First Run
⌄
Run this the first time to build your wiki from scratch. Replace [time period] with how long you have been using AI tools.
seed prompt
I have placed all my exported AI conversations in /raw.
These are real conversations I have had over the past [time period].
Please read through everything and build me a wiki that captures:
1. My professional interests and areas of expertise
2. Business ideas and projects I have worked on
3. Recurring themes in how I think and work
4. Key decisions I have made and the reasoning behind them
5. People, tools, and frameworks I reference frequently
Create organized wiki pages with backlinks between related ideas.
Write each page as a reference article: factual, clear, third-person where appropriate.
CompileCompile: Add New Material
⌄
Run this whenever you add new files to your raw folder. Claude integrates them into the existing wiki without overwriting what is already there.
compile prompt
I have added new files to /raw. Please:
1. Read all unprocessed files
2. For each file, extract key information and integrate it into the wiki
3. Update any existing wiki pages that are relevant
4. Create new concept pages for any topics not yet covered
5. Add backlinks and cross-references between related pages
6. Note any contradictions with existing pages
7. Mark processed files with a frontmatter tag: compiled: true
LintLint: Monthly Health Check
⌄
Run this once a month to keep your wiki healthy. Finds orphan pages, contradictions, stale claims, and gaps.
lint prompt
Review my entire wiki and:
1. Find pages that contradict each other
2. Identify orphan pages (pages with no links pointing to them)
3. Find concepts referenced across multiple pages that do not have their own page yet
4. Suggest 5 new articles I should have Claude write based on gaps
5. Flag any outdated information based on newer sources in raw
QueryCross-Source Synthesis
⌄
Ask Claude to reason across your entire knowledge base. This is where the compounding value shows up.
synthesis prompt
Based on everything in my wiki, what are the most important themes
or patterns that appear consistently across my thinking and work?
Synthesize across all relevant pages and give me a structured analysis.
Cite which wiki pages you are drawing from.
QueryGaps Query: Self-Improving Loop
⌄
Your second brain tells you what it needs to grow. Run this to generate your next reading and research agenda.
gaps prompt
What are the gaps in my wiki right now?
What knowledge is underrepresented that I should research and add?
Give me a prioritized list of 5 to 10 topics worth exploring next.
QueryDecision Review
⌄
Surface patterns in how you have made choices over time.
decision prompt
Based on my wiki, what patterns do I see in the decisions I have made?
Where have I been consistent? Where have I been inconsistent?
What does my history suggest I should do differently going forward?
AutomateAutomate: Inbox Processor
⌄
Daily routine that checks /raw/inbox, parses new files, updates the wiki, and moves processed files to /raw/processed. Pair with the two-folder pattern from Module 05.
inbox processor prompt
Check /raw/inbox for any new files. If the folder is empty, exit and do nothing.
For each file found, in order:
1. Identify the file type: Claude export, ChatGPT export, meeting
transcript, or general document
2. Extract key entities: decisions made, people mentioned, projects
discussed, tools referenced, ideas that recurred across the conversation
3. For each entity, check if a wiki page already exists. If yes, add new
information without overwriting existing content. If no, create a new page.
4. Add bidirectional [[wikilinks]] between new content and related pages
5. Move the file from /raw/inbox to /raw/processed
When complete, print: files processed, wiki pages created, wiki pages updated.
AuditAudit: Vault Graph Health
⌄
Scans the vault, calculates connectivity stats, finds orphaned notes, scores candidate connections, and writes a health report. Run monthly. See Module 07 for the full walkthrough.
graph health prompt
Scan every .md file in this vault. Build a complete directed link graph.
Calculate and report:
- Total notes scanned
- Total note-to-note links
- Average in-degree (incoming links per note)
- Notes with zero incoming links
- True orphans (zero in AND zero out, minimum 100 words)
For each true orphan and each note with fewer than 2 incoming links:
- Find the 5 most similar notes using keyword overlap
- Score similarity 0–1
- List the top shared terms
Write everything to /outputs/vault-graph-health.md using this structure:
## Stats
[table of metrics]
## True Orphans
[list with candidates]
## Near-Orphans
[list with candidates]
Do not modify any other files.
AnalysisCareer Interest Framework
⌄
Run three career frameworks (LINK Test, Sorting Hat, Vesting Schedule) against your entire vault. Outputs a Markdown report identifying your compounding interest pairs, what each interest does for you professionally, and where your attention is actually going vs. where you say it is. Best run on a vault with at least a few months of real history.
interest framework prompt
Vault directory: [paste your vault path here, or Claude will scan automatically]
Weight notes from the last 90 days (verify today's date) more heavily.
You are analyzing my Obsidian vault to run three career/interest frameworks.
SETUP
1. Recursively scan the vault directory I give you (and any linked folders).
2. Parse all .md files, notes, project files, meeting transcripts, journal
entries, and any text-based documents.
3. Build a master list of every distinct interest, skill, domain, role,
project, or identity mentioned across my notes. Examples: job titles,
tools I use, hobbies, side projects, client work, reading topics, courses,
ideas I return to repeatedly.
FRAMEWORK 1: THE LINK TEST
For every pair of interests/domains (focus on the top 10-15 most frequent):
Score them on the LINK rubric:
L (Language): Do I ever describe one using the other's vocabulary?
I (Improve): Is there evidence that growth in one made the other better?
N (Need): Do I use tools/concepts from one to solve problems in the other?
C (Cut): Would removing one visibly hurt the other based on how I operate?
Score each 0-4. Output a table:
Interest A | Interest B | L | I | N | C | Total | Verdict
Verdict options: Competing / Adjacent / Compounding
Highlight the highest-scoring pairs. These are my natural M-shapes.
FRAMEWORK 2: THE SORTING HAT
For each interest/domain, analyze my notes to assign it a job:
GOOD AT: Evidence I have genuine skill or a track record here
STABILITY: This generates or protects income/security
OPTIONALITY: This opens future doors or increases my leverage
RESTORES: Evidence this gives me energy, joy, or recovery
An interest can hold multiple jobs.
Flag any interests that hold ZERO jobs. These are candidates to cut or park.
Output a table:
Interest | Good At | Stability | Optionality | Restores | Jobs Count | Recommendation
FRAMEWORK 3: THE VESTING SCHEDULE
For each interest that earned at least one job in Framework 2:
Assess its current stage based on note frequency, recency, and depth:
ACTIVELY INVESTING: Recent heavy engagement, still building capability
VESTED/HARVESTING: Solid baseline achieved, occasional use, not growing
DORMANT: Past interest, rarely mentioned, no recent activity
EMERGING: New interest, appearing more frequently in recent notes
Recommend: Invest More / Maintain / Harvest / Cut / Watch
Output a table:
Interest | Stage | Evidence | Recommendation
FINAL SYNTHESIS
1. Name my top 2-3 compounding stacks (interests that reinforce each other)
2. Identify my "golden thread" -- the invisible connector across my interests
3. Flag 2-3 interests I should consider cutting or parking based on the data
4. Suggest how my M-shape could be positioned professionally given the current
season my notes suggest I am in
OUTPUT FORMAT
Save a single Markdown report as /outputs/interest-framework-analysis.md.
Use clear headers for each framework.
Include an executive summary at the top (5-7 sentences max).
Be direct. If something is competing for my time without compounding, say so.
NOTES ON INTERPRETATION
- Weight recent notes (last 90 days) more heavily than older ones
- Repeated mentions across different contexts (meetings, journals, projects)
signal stronger investment than single mentions
- Look for language crossover: am I using marketing terms in engineering notes,
or systems thinking in creative work? That is evidence of compounding.
Start by listing all interests/domains you found. I will confirm or add to
the list before you run the frameworks.
AuditAudit: Duplicate Detector
⌄
Scans your vault for near-identical notes, scores their similarity, and presents merge or delete recommendations for review before anything is changed.
When to use: After importing a large batch of exports, after multi-source merging, or any time your vault feels bloated. Also useful after your first compile if Claude created multiple pages for the same concept under slightly different names.
duplicate detector prompt
Scan every .md file in this vault and identify potential duplicates.
Do not modify any files during this step.
## Pass 1: Title Similarity
Find notes with titles that are close but not identical. Examples:
- "Client Onboarding" and "Onboarding Process" and "New Client Onboarding"
- "Q4 Strategy" and "Q4 Strategic Plan" and "Strategy Q4"
- "Michael Wagner" and "Mike Wagner" and "Wags"
List every suspicious pair or cluster with their file paths.
## Pass 2: Content Similarity
For each pair flagged in Pass 1, compare their actual content:
- What percentage of the key topics overlap?
- Does one contain information the other doesn't?
- Do they contradict each other on any facts?
- When was each last modified?
Score each pair 0–100 for duplication confidence:
- 90–100: Almost certainly the same note (safe to auto-merge)
- 70–89: Heavy overlap, likely duplicate (recommend merge, review first)
- 50–69: Partial overlap (recommend linking, not merging)
- Below 50: Coincidentally similar (probably fine, flag for awareness)
## Pass 3: Orphan Variants
Check for notes that appear to be incomplete versions or early drafts
of a more complete page — same topic, much shorter, no incoming links.
These are candidates for deletion rather than merging.
## Output Format
Write your findings to /outputs/duplicate-report.md:
### High Confidence Duplicates (90–100)
| Note A | Note B | Score | Recommendation |
### Likely Duplicates (70–89)
| Note A | Note B | Score | Overlap | Unique to A | Unique to B |
### Partial Overlap (50–69)
| Note A | Note B | Score | Recommended Action |
### Orphan Variants
| Short Note | Parent Note | Recommendation |
Do not merge, delete, or modify anything yet. Output the report only.
Step 2 — After reviewing /outputs/duplicate-report.md
apply decisions prompt
I've reviewed /outputs/duplicate-report.md and I'm ready to act on the findings.
For each item I approve below, take the following action:
MERGE: Combine both notes into one. Keep the canonical name from
entity-map.md if it exists, otherwise keep the longer/more complete
title. Move all unique content from both into the merged page.
Add a note at the top: "Merged from: [original filenames]".
Delete the duplicate file after merging.
LINK: Do not merge. Instead add a [[wikilink]] in both notes pointing
to each other under a ## Related section.
DELETE: The note is a stub or early draft with no unique content.
Delete it and update any links pointing to it to point to the
parent note instead.
SKIP: Leave both notes unchanged.
Here are my decisions:
[paste rows from /outputs/duplicate-report.md with your decision next to each]
After executing, print a summary: merged, linked, deleted, skipped.
Then run the Vault Graph Health audit prompt to confirm connectivity
improved.
CaptureCapture: Raw Note Processor
⌄
Takes a messy voice transcript or quick mobile note and extracts what's worth keeping — core insight, decisions, people/projects mentioned, action items, and a recommendation on where it belongs in the wiki. Use this when a raw capture is too rough for the standard inbox automation. See Bonus Module for the full mobile capture setup.
raw note processor prompt
I have a raw capture — a voice transcript or quick mobile note. It is
messy, incomplete, and unformatted. Do not clean up or polish it.
Instead, extract what is worth keeping.
Raw capture:
[paste your voice transcript or mobile note here]
Extract:
1. The core idea or insight in one clear sentence
2. Any decisions made or conclusions reached
3. Any people, projects, or topics mentioned that have wiki pages
4. Any action items or follow-ups implied
5. Any questions that need answering
Then: is this worth a new wiki page, an addition to an existing page,
or just a note filed in /wiki/journal? Recommend one and explain why
in one sentence.
Do not write the wiki page yet — give me the extraction first.
SafetyDry-Run Safety Check
⌄
Run this before any operation that touches a lot of files — compile, lint, merge, graph health fix. Claude lists every file it would create, modify, rename, or delete, and flags anything risky. Nothing changes until you confirm. See Module 10 for the full safety setup.
dry-run prompt
Before I run the following operation, I want a full preview of what
you would do. Do NOT make any changes yet.
Operation I am about to run: [paste the prompt you are planning to use]
For each action you would take, list:
1. What file would be affected (created, modified, renamed, or deleted)
2. What the change would be (new content, overwrite, append, rename to what)
3. Whether the change is reversible with git restore if I change my mind
Group by: files that would be created / files that would be modified /
files that would be deleted or renamed.
At the end, flag anything that looks risky — large overwrites, deletions,
or changes to files that are heavily linked.
Wait for my confirmation before proceeding.
DraftDraft: From Past Work
⌄
Give Claude a new brief and it searches your vault for relevant past documents — grants, proposals, memos, briefs — extracts what worked and what didn't, and hands you a structured foundation before you write a word. See Module 09 for the full walkthrough.
draft from history prompt
I need to write: [describe the document — type, audience, goal, length]
Search my vault for past work that is similar in any of these dimensions:
- Same document type (grant, proposal, memo, brief, report)
- Same audience or funder
- Same topic or domain
- Same stakes or context
For each relevant past document found:
1. Summarize what I argued and how I structured it
2. Note anything that worked well (funded, approved, well-received) based
on my notes
3. Note anything that didn't land, if there is evidence of that
4. Extract the 3–5 strongest sentences or passages I could adapt
Then give me a recommended structure for the new document based on what
has worked before. Do not write the document yet — give me the foundation
and wait for my confirmation before drafting.
QueryDigital Twin: Pressure Test
⌄
Describe an idea or direction and Claude argues back using evidence from your own vault — your past positions, decisions, and outcomes. Not general devil's advocate. Your specific history, cited.
digital twin prompt
I am considering: [describe the idea, direction, or decision]
Before I commit to this, search my vault and do the following:
1. Find every time I have addressed a similar idea, direction, or decision
in my notes — even if the framing was different
2. Identify my past position: was I for it, against it, or ambivalent?
Cite the note and approximate date
3. Check for contradictions: does this new direction conflict with a
position I have held or a commitment I have made?
4. Look for relevant past outcomes: have I tried something adjacent before?
What happened?
5. Play devil's advocate using only evidence from my own notes — not
general reasoning, but things I have actually written or documented
End with: what does my own history suggest I should think carefully about
before moving forward?
AutomateAgent Knowledge Layer
⌄
System prompt template for wiring any Claude agent (or compatible open-source agent) to your second brain wiki. The agent reads your vault as its source of truth and cites which page it drew from. Customize the role for your use case: SOP assistant, grant researcher, onboarding guide.
agent system prompt template
You are [role — e.g. "a process assistant for our team" / "a grant
research assistant" / "an onboarding guide"].
Your knowledge base is a second brain wiki located at [vault path].
Before answering any question, read the relevant wiki pages. The wiki
is the source of truth — prefer it over your training data whenever
the two conflict.
Wiki structure:
- /wiki/concepts — topic articles and frameworks
- /wiki/people — key contacts and context
- /wiki/projects — active and past project summaries
- /wiki/decisions — decisions made and reasoning
- schema.md — naming conventions and page format rules
Rules:
- Cite the wiki page you drew from when answering
- If the wiki does not contain an answer, say so explicitly —
do not invent information
- Do not modify or delete any wiki files unless explicitly instructed
- Flag anything that appears outdated or contradictory for human review
Your role: [describe the specific job — answer team process questions,
assist with grant applications, brief new clients, etc.]
Download the Full Prompt Library
All 15 prompts as a Markdown file, ready to drop into your vault.