Merge remote-tracking branch 'origin/main'

Bootstrap script for this vault.md

@@ -79,41 +79,28 @@ 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
 
-  
-
 ```bash
-
 git clone <GITEA_REPOSITORY_URL>
-
 cd SecondBrain
+```
 
 ## 2. Restore the folder structure
 
+```bash
 ./scripts/bootstrap-vault.sh
+```
 
 ## 3. Open the vault in Obsidian
 
@@ -123,87 +110,141 @@ Open Obsidian and choose:
 
 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.
+
 ---
 
-# Required Obsidian Plugins
+# Obsidian Plugins
 
-Install and enable:
+## Core Workflow
 
-- Templater
+These plugins are important to the functionality of SecondBrain.
-- Dataview
-- Obsidian Git
 
-Check `10 Knowledge/Templates` for the templates used by the system.
+### Templater
 
-Important machine-specific Obsidian files such as `workspace.json` are intentionally not synchronized.
+Used for dynamic note creation, automatic file naming, folder creation, dates, and structured templates.
+
+Templates are stored in:
+
+```text
+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
 
+```text
 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:
 
+```text
 20 Work/Team/
-
 └── Employee Name/
-
     └── 1-1/
-
         └── 08/
+```
 
 ---
 
@@ -213,80 +254,92 @@ MeetMic is used for local meeting transcription and/or summaries.
 
 MeetMic should output Markdown or transcript files into:
 
+```text
 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 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:
     
+
+```text
 <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.
+Contract PDFs are deliberately **not stored inside the Obsidian vault**.
 
 The local contract processor lives separately, typically at:
 
+```text
 ~/Herd/scripts/obsidian-contracts
+```
 
 Expected source structure:
 
+```text
 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:
 
+```text
 Directus/2026/
+```
 
 will generate:
 
+```text
 Directus - 2026-2027.md
+```
 
 even if the contract itself names TFO as the purchaser.
 
 Generated contract notes are written to:
 
+```text
 20 Work/Contracts/Active/
+```
 
 ---
 
@@ -296,27 +349,41 @@ Generated contract notes are written to:
 
 Create a virtual environment:
 
+```bash
 cd ~/Herd/scripts/obsidian-contracts
 
-  
-
 python3 -m venv .venv
-
 source .venv/bin/activate
 
-Install dependencies:
-
 pip install requests python-dotenv
+```
 
-## PDF extraction
+When returning to the project later:
+
+```bash
+cd ~/Herd/scripts/obsidian-contracts
+source .venv/bin/activate
+```
+
+When finished:
+
+```bash
+deactivate
+```
+
+## PDF Extraction
 
 Install Poppler:
 
+```bash
 brew install poppler
+```
 
 This provides:
 
+```text
 pdftotext
+```
 
 ## Local AI
 
@@ -324,63 +391,69 @@ Ollama is used for local contract extraction.
 
 Install Ollama and confirm:
 
+```bash
 ollama --version
+```
 
 The current contract model is:
 
+```text
 contract-reader
+```
 
 Example base model:
 
+```text
 qwen3:1.7b
+```
 
 The dedicated model should use a limited context to avoid excessive memory usage.
 
-Example Modelfile:
+Example `Modelfile`:
 
+```text
 FROM qwen3:1.7b
 
-  
-
 PARAMETER num_ctx 4096
-
 PARAMETER temperature 0.1
-
 PARAMETER num_predict 1200
+```
 
 Create it:
 
+```bash
 ollama create contract-reader -f Modelfile
+```
 
 ---
 
 # Contract Processor Environment
 
-The local `.env` file is NOT committed to Git.
+The local `.env` file is **not committed to Git**.
 
 Example:
 
+```text
 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"
+```
 
-Then process one contract:
+Process one contract:
 
+```bash
 python3 process_contracts.py --folder Algolia/2024
+```
 
 Force regeneration:
 
+```bash
 python3 process_contracts.py --folder Algolia/2024 --force
+```
 
 ---
 
@@ -389,69 +462,93 @@ python3 process_contracts.py --folder Algolia/2024 --force
 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:
 
+```text
 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 Ignore
+# Git Configuration
 
-Recommended `.gitignore` entries:
+## Recommended `.gitignore`
 
+```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:
 
+```gitignore
 .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:
+
+```text
+.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:
+
+```text
+.obsidian/workspace-mobile.json
+```
 
 ---
 
@@ -460,56 +557,126 @@ credentials.json
 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:
 
+```text
 SecondBrain
-
+└── Obsidian content, templates, configuration and structure
-└── Obsidian content, templates 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:
 
-- [ ]  Install Git
+## Vault
-- [ ]  Clone SecondBrain from Gitea
+
-- [ ]  Run `bootstrap-vault.sh`
+-  Install Git
-- [ ]  Install Obsidian
+    
-- [ ]  Install Templater
+-  Clone SecondBrain from Gitea
-- [ ]  Install Dataview
+    
-- [ ]  Install Obsidian Git
+-  Run `bootstrap-vault.sh`
-- [ ]  Configure MeetMic output
+    
-- [ ]  Install Python
+-  Install Obsidian
-- [ ]  Install Poppler
+    
-- [ ]  Install Ollama
+-  Open SecondBrain as a vault
-- [ ]  Restore/create `contract-reader`
+    
-- [ ]  Clone/copy contract automation scripts
+
-- [ ]  Recreate `.env`
+## Obsidian Plugins
-- [ ]  Test contract extraction
+
-- [ ]  Test Git pull/push
+-  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