SecondBrain/Bootstrap script for this vault.md

Use this bootstrap-vault.sh:

#!/bin/bash

set -e

echo ""
echo "======================================"
echo " SecondBrain Vault Bootstrap"
echo "======================================"
echo ""

folders=(
  "00 Inbox/MeetMic"

  "10 Knowledge/CTO Academy/Data"
  "10 Knowledge/CTO Academy/Project Management"
  "10 Knowledge/CTO Academy/Infrastructure"
  "10 Knowledge/CTO Academy/Security"
  "10 Knowledge/Quotes"
  "10 Knowledge/Templates"

  "20 Work/Contracts/Active"
  "20 Work/Contracts/Archive"

  "20 Work/Decisions"
  "20 Work/Ideas"
  "20 Work/Journal"
  "20 Work/KPIs"

  "20 Work/Meetings/Internal"
  "20 Work/Meetings/Vendors"

  "20 Work/Projects"
  "20 Work/Team"
  "20 Work/Tracking"
  "20 Work/Weekly Review"

  "90 Archives"
)

for folder in "${folders[@]}"; do
  mkdir -p "$folder"

  if [ ! -f "$folder/.gitkeep" ]; then
    touch "$folder/.gitkeep"
  fi

  echo "✓ $folder"
done

echo ""
echo "Vault structure created."
echo ""

echo "Important:"
echo "- Employee folders under 20 Work/Team are created dynamically by Templater."
echo "- Month folders under employee 1-1 folders are also created dynamically."
echo "- Templates themselves should already exist in Git under 10 Knowledge/Templates."
echo ""

echo "SecondBrain bootstrap complete."
echo ""

Save it as:

scripts/bootstrap-vault.sh

Then:

chmod +x scripts/bootstrap-vault.sh

And commit it.

---

For the README, I’d use something like this:

SecondBrain

Personal work and leadership knowledge system built with Obsidian.

The vault is backed up through Git and a private Gitea repository.

The goal is to make the environment easy to restore on a new computer with minimal manual reconstruction.

---

Quick Restore

1. Clone the vault

git clone <GITEA_REPOSITORY_URL>
cd SecondBrain

2. Restore the folder structure

./scripts/bootstrap-vault.sh

3. Open the vault in Obsidian

Open Obsidian and choose:

Open folder as vault

Select the cloned SecondBrain directory.

4. Restore plugins

Enable Community Plugins in Obsidian and install the plugins listed below.

Some plugin configuration is stored in .obsidian/ and may already be restored by Git depending on what is tracked.

Machine-specific workspace state is intentionally excluded.

---

Obsidian Plugins

Core Workflow

These plugins are important to the functionality of SecondBrain.

Templater

Used for dynamic note creation, automatic file naming, folder creation, dates, and structured templates.

Templates are stored in:

10 Knowledge/Templates/

Important: YAML/frontmatter must remain at the very beginning of templates. Do not place Templater JavaScript before the YAML block.

Dataview

Used to generate dynamic lists and views from note properties and metadata.

Obsidian Git

Provides Git integration and automatic backup from the desktop vault.

Repository synchronization is done against a private Gitea repository.

Auto GitKeep

Automatically creates .gitkeep files inside empty directories so the vault structure can be preserved by Git.

This is particularly useful because Git does not normally track empty directories.

---

Navigation and Editing

These plugins improve the Obsidian interface but are not required for the underlying vault structure.

Notebook Navigator

Replaces the standard Obsidian file explorer with a two-pane navigation interface.

Folder Links

Allows folder links to reveal the corresponding folder in the navigation interface.

Editing Toolbar

Provides a more visual editing toolbar with commonly used Markdown commands.

Iconic

Adds custom icons to folders, files, properties, bookmarks, and other Obsidian interface elements.

Omnisearch

Provides enhanced full-vault search.

---

Integration

Local REST API with MCP

Provides a local REST API and MCP interface for interacting with the vault from external tools and local automation.

This is an advanced integration and is not required for basic vault operation.

Do not expose the REST API directly to the public Internet.

---

Optional / Disabled Plugins

Settings Search

Provides search across Obsidian settings.

Currently installed but disabled.

---

Vault Structure

00 Inbox/
└── MeetMic/

10 Knowledge/
├── CTO Academy/
├── Quotes/
├── Templates/
└── Principles.md

20 Work/
├── Contracts/
│   ├── Active/
│   └── Archive/
├── Decisions/
├── Ideas/
├── Journal/
├── KPIs/
├── Meetings/
│   ├── Internal/
│   └── Vendors/
├── Projects/
├── Team/
├── Tracking/
└── Weekly Review/

90 Archives/

Employee and monthly 1-1 folders are created dynamically by Templater.

Example:

20 Work/Team/
└── Employee Name/
    └── 1-1/
        └── 08/

---

MeetMic Integration

MeetMic is used for local meeting transcription and/or summaries.

MeetMic should output Markdown or transcript files into:

00 Inbox/MeetMic/

The Inbox is intentionally a temporary landing area.

After reviewing a MeetMic note:

• move useful meeting information into 20 Work/Meetings

• extract decisions into 20 Work/Decisions

• extract action items into Jira, Twos, or Monday

• delete/archive the raw MeetMic output when no longer useful

MeetMic Machine Setup

MeetMic itself is not stored in this vault.

On a new computer:

1. Install MeetMic.

2. Configure its output folder to point to:

<VAULT_PATH>/00 Inbox/MeetMic

3. Confirm Markdown output is enabled.

4. Test with a short recording.

---

Contract Processing Integration

Contract PDFs are deliberately not stored inside the Obsidian vault.

The local contract processor lives separately, typically at:

~/Herd/scripts/obsidian-contracts

Expected source structure:

obsidian-contracts/
├── Algolia/
│   └── 2024/
│       └── contract.pdf
├── Directus/
│   └── 2026/
│       └── contract.pdf
├── process_contracts.py
├── prompt.md
├── .env
└── logs/

The vendor folder name is the canonical vendor name.

Example:

Directus/2026/

will generate:

Directus - 2026-2027.md

even if the contract itself names TFO as the purchaser.

Generated contract notes are written to:

20 Work/Contracts/Active/

---

Contract Processor Requirements

Python

Create a virtual environment:

cd ~/Herd/scripts/obsidian-contracts

python3 -m venv .venv
source .venv/bin/activate

pip install requests python-dotenv

When returning to the project later:

cd ~/Herd/scripts/obsidian-contracts
source .venv/bin/activate

When finished:

deactivate

PDF Extraction

Install Poppler:

brew install poppler

This provides:

pdftotext

Local AI

Ollama is used for local contract extraction.

Install Ollama and confirm:

ollama --version

The current contract model is:

contract-reader

Example base model:

qwen3:1.7b

The dedicated model should use a limited context to avoid excessive memory usage.

Example Modelfile:

FROM qwen3:1.7b

PARAMETER num_ctx 4096
PARAMETER temperature 0.1
PARAMETER num_predict 1200

Create it:

ollama create contract-reader -f Modelfile

---

Contract Processor Environment

The local .env file is not committed to Git.

Example:

OBSIDIAN_VAULT="/Users/YOUR_USER/Documents/Obsidian Vault/SecondBrain"
CONTRACT_OUTPUT="20 Work/Contracts/Active"

OLLAMA_BASE_URL="http://127.0.0.1:11434"
OLLAMA_MODEL="contract-reader"

MAX_CONTEXT_CHARS="5000"

Process one contract:

python3 process_contracts.py --folder Algolia/2024

Force regeneration:

python3 process_contracts.py --folder Algolia/2024 --force

---

Contract Processor Behavior

The processor:

1. extracts PDF text locally using pdftotext

2. reduces the contract to important sections

3. sends only those excerpts to local Ollama

4. extracts commercial and renewal information

5. validates important renewal clauses against the actual PDF text

6. creates an Obsidian Markdown contract record

Nothing is intentionally sent to a cloud AI provider.

Important renewal fields include:

auto_renewal
renewal_term_months
customer_notice_days
vendor_notice_days
notice_deadline
renewal_increase_percent
renewal_pricing_rule

The generated note also contains source evidence from the PDF.

---

Git Configuration

Recommended .gitignore

# macOS
.DS_Store

# Obsidian machine-specific state
.obsidian/workspace.json
.obsidian/workspace-mobile.json

# PDFs should never be stored in the vault repository
*.pdf

The contract automation repository should additionally ignore:

.env
.venv/
logs/
token.json
credentials.json
*.pdf

.obsidian Strategy

Do not ignore the entire .obsidian/ directory.

Keeping selected Obsidian configuration in Git makes it much easier to reproduce the vault on another computer.

Machine-specific state such as the following should remain ignored:

.obsidian/workspace.json
.obsidian/workspace-mobile.json

Plugin configuration can be synchronized where appropriate.

---

Mobile

The mobile vault may use GitSync rather than the Obsidian Git community plugin.

Mobile and desktop should synchronize against the same private Gitea repository.

Avoid making conflicting edits to the same note simultaneously on multiple devices.

Machine-specific mobile workspace state is excluded through:

.obsidian/workspace-mobile.json

---

What Is NOT Backed Up By This Vault

The following must be restored separately:

• Ollama models

• MeetMic application/settings

• contract PDFs

• ~/Herd/scripts/obsidian-contracts unless stored in its own private repository

• .env

• authentication tokens

• local application settings

• Git/Gitea credentials

• GitSync application configuration

---

Recommended Recovery Strategy

Maintain two private Git repositories:

SecondBrain
└── Obsidian content, templates, configuration and structure

obsidian-automation
└── scripts, prompts, Modelfiles and setup documentation

Never commit:

• contracts

• PDFs

• secrets

• .env

• authentication tokens

---

Recovery Checklist

After moving to a new computer:

Vault

• Install Git

• Clone SecondBrain from Gitea

• Run bootstrap-vault.sh

• Install Obsidian

• Open SecondBrain as a vault

Obsidian Plugins

• Install Templater

• Install Dataview

• Install Obsidian Git

• Install Auto GitKeep

• Install Notebook Navigator

• Install Folder Links

• Install Editing Toolbar

• Install Iconic

• Install Omnisearch

• Install Local REST API with MCP

• Verify Templater template folder

• Verify Git configuration

• Verify plugin settings

Integrations

• Configure MeetMic output

• Install Python

• Install Poppler

• Install Ollama

• Restore/create contract-reader

• Clone/copy contract automation scripts

• Recreate .env

• Test contract extraction

Synchronization

• Test Git pull

• Test Git commit/push

• Configure GitSync on mobile if required

• Test mobile pull

• Test mobile push