Research-Stack/obsidian-vault/README.md

Obsidian Vault - Research Stack Knowledge Base

Overview

This Obsidian vault serves as the central knowledge management system for the Sovereign Research Stack. It provides structured organization of formal proofs, attack plans, milestones, receipts, and research artifacts across all 7 layers of the USTSM architecture.

🗂️ Vault Structure

obsidian-vault/
├── 00-MAP/                    # Navigation & orientation
│   ├── README.md              # This file - start here!
│   ├── Dashboard.md           # System health dashboard
│   ├── Core Concepts.md       # Fundamental principles
│   ├── Getting Started.md     # How to use this vault
│   └── Glossary.md            # Terminology reference
│
├── 01-LAYERS/                 # Layered knowledge (L0-L6)
│   ├── 00-Overview.md         # USTSM architecture overview
│   ├── L0-Primordial/         # Pure math, fixed-point arithmetic
│   ├── L1-Geometric/          # Shape-aware topology
│   ├── L2-Biological/         # Genetic codes, neurons
│   ├── L3-Thermodynamic/      # Energy-aware quality
│   ├── L4-Security/           # Attack-aware gating
│   ├── L5-Semantic/           # Meaning-aware filtering
│   └── L6-Meta/              # Self-aware adaptation
│
├── 07-RESEARCH/               # Active research
│   ├── 00-Milestones/         # Project milestones
│   ├── 01-Attack-Plans/       # Research attack plans
│   ├── 02-Conjectures/        # Research conjectures
│   └── 03-Experiments/        # Experimental validation
│
├── 08-TOOLS/                  # Tools & automation
│   ├── 00-Scripts/            # Automation scripts
│   ├── 01-Templates/          # Document templates
│   └── 02-Workflows/         # Research workflows
│
├── 09-REFERENCES/            # External references
│   ├── assets/                # Images, diagrams, files
│   ├── bibliography/          # Academic references
│   └── external-links/        # Useful external resources
│
├── 10-ARCHIVE/               # Completed/completed items
│   ├── completed-milestones/
│   ├── old-attack-plans/
│   └── historical-receipts/
│
└── .obsidian/                 # Obsidian configuration
    ├── community-plugins.json # Plugin settings
    ├── snippets/              # CSS customizations
    ├── templates/             # Templater configurations
    └── workspaces.json        # Workspace layouts

🚀 Getting Started

1. Opening the Vault

1. Install Obsidian on your system
2. Open Obsidian and select "Open folder as vault"
3. Navigate to /home/researcher/stack/obsidian-vault/
4. The vault will load with all configurations and plugins

2. Essential Navigation

• Start Here: Open 00-MAP/README.md for orientation
• Dashboard: Open 00-MAP/Dashboard.md for system overview
• Graph View: Use Ctrl/Cmd+G to see the knowledge graph
• Quick Switcher: Use Ctrl/Cmd+O to quickly open files
• Command Palette: Use Ctrl/Cmd+P for all commands

3. Using Templates

Templates are available for common research artifacts:

Template	Use For	Location
Formal Proof	New Lean theorems	08-TOOLS/01-Templates/Formal Proof.md
Attack Plan	Research initiatives	08-TOOLS/01-Templates/Attack Plan.md
Milestone	Project milestones	08-TOOLS/01-Templates/Milestone.md
Receipt	Receipt documents	08-TOOLS/01-Templates/Receipt.md
Daily Standup	Daily progress	08-TOOLS/01-Templates/Daily Standup.md

To use a template:

1. Press Alt+Shift+F (or your configured hotkey)
2. Select the template type
3. Fill in the requested information
4. The note will be created with proper structure

4. QuickAdd Commands

Press Ctrl+Shift+P to access QuickAdd commands:

• Create Formal Proof - Quickly create a new formal proof
• Create Attack Plan - Start a new attack plan
• Create Milestone - Add a new milestone
• Create Receipt - Generate a receipt document
• Capture Research Note - Quick note capture
• Generate Lean Stub - Insert Lean code template
• Add Progress Update - Update progress on current file

🎨 Customization

Themes & Styling

The vault includes a custom CSS snippet (research-stack.css) with:

• Layer-specific colors (L0-L6)
• Formal proof highlighting
• Receipt styling
• Mathematical expression formatting
• Graph view customization

To enable the theme:

1. Go to Settings → Appearance
2. Select "Research Stack" from the theme dropdown

Workspaces

Pre-configured workspaces for different activities:

• Dashboard - Overview of all system metrics
• Formal Methods - For proof development
• Research Planning - For milestone and attack plan management
• Hardware Design - For hardware extraction work

To switch workspaces:

1. Open Command Palette (Ctrl/Cmd+P)
2. Type "Workspaces: Load"
3. Select the desired workspace

📊 Dataview Queries

The vault uses Dataview plugin for dynamic content:

Dashboard Queries

• Build Status - Shows formal proof compilation status
• Active Attack Plans - Lists in-progress attack plans
• Recent Receipts - Shows recently generated receipts
• Milestone Progress - Tracks milestone completion

Custom Queries

You can create custom queries using Dataview syntax:

TABLE status, priority, layer
FROM #attack-plan
WHERE status = "active"
SORT priority DESC

🔗 Key Relationships

Cross-References

The vault uses wiki-links ([[filename]]) for internal connections:

• Formal Proofs → Receipts (each proof generates receipts)
• Attack Plans → Milestones (plans contain milestones)
• Milestones → Formal Proofs (milestones require proofs)
• Experiments → Receipts (experiments generate validation receipts)

Tag System

Organized tags for filtering:

• #layer-L0 through #layer-L6 - Layer classification
• #formal-proof - Mathematical proofs
• #receipt - Validation receipts
• #attack-plan - Research initiatives
• #milestone - Project milestones
• #conjecture - Research hypotheses
• #experiment - Experimental work

🔧 Plugin Configuration

Installed Plugins

Plugin	Purpose	Status
Templater	Template automation	✅ Enabled
QuickAdd	Quick note creation	✅ Enabled
Dataview	Dynamic queries	✅ Enabled
Advanced Tables	Table formatting	✅ Enabled
Excalidraw	Diagram creation	✅ Enabled
Canvas	Visual organization	✅ Enabled
Tag Wrangler	Tag management	✅ Enabled
Breadcrumbs	Navigation aid	✅ Enabled
Workspaces	Layout management	✅ Enabled

Plugin Settings

All plugins are pre-configured. To modify settings:

1. Open Settings (Ctrl/Cmd+,)
2. Go to Community Plugins
3. Select the plugin to configure

📝 Contributing

Adding New Content

1. Use the appropriate template for the content type
2. Follow the established naming conventions
3. Add relevant tags for discoverability
4. Link to related documents using wiki-links

Updating Existing Content

1. Open the file to edit
2. Make your changes
3. Update the modified date in frontmatter
4. Add update notes in the file if significant

Creating New Templates

1. Copy an existing template as a starting point
2. Modify the structure and prompts
3. Save to 08-TOOLS/01-Templates/
4. Update Templater settings to recognize the new template

🔄 Maintenance

Regular Tasks

• Daily: Update active attack plans and milestones
• Weekly: Review dashboard metrics and progress
• Monthly: Archive completed items to 10-ARCHIVE/
• Quarterly: Review and update template structures

Backup

The vault is part of the Research Stack repository. Regular commits ensure backup:

git add obsidian-vault/
git commit -m "Update: [description of changes]"

🆘 Troubleshooting

Common Issues

Issue: Plugins not loading
Solution: Go to Settings → Community Plugins → Turn on "Safe mode" then back off

Issue: Templates not working
Solution: Check Templater settings → Template folder location → Should be 08-TOOLS/01-Templates/

Issue: Dataview queries not updating
Solution: Use Ctrl/Cmd+P → "Dataview: Force refresh all views"

Issue: Graph view empty
Solution: Check that files have content and links - empty files won't appear

Getting Help

• Check 00-MAP/Getting Started for detailed walkthroughs
• Review 00-MAP/Core Concepts for terminology
• Look at existing documents for examples of proper formatting

📚 Additional Resources

Internal Documentation

• 00-MAP/Core Concepts - Fundamental principles
• 00-MAP/Glossary - Terminology reference
• 01-LAYERS/00-Overview - USTSM architecture
• 08-TOOLS/02-Workflows - Research workflows

External Resources

• Obsidian Help
• Dataview Documentation
• Templater Documentation
• Research Stack Repository

📊 Vault Statistics

Content Overview

• Total Notes: [Auto-generated]
• Formal Proofs: [Auto-generated]
• Attack Plans: [Auto-generated]
• Milestones: [Auto-generated]
• Receipts: [Auto-generated]

Activity Metrics

• Last Updated: [Auto-generated]
• Files Modified Today: [Auto-generated]
• New This Week: [Auto-generated]

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🎯 Quick Actions

For Formal Methods Work

1. Open workspace: "Formal Methods"
2. Create new proof: Alt+Shift+F → "Formal Proof"
3. Link to related proofs using [[...]]
4. Generate receipt when complete

For Research Planning

1. Open workspace: "Research Planning"
2. Create attack plan: Alt+Shift+F → "Attack Plan"
3. Add milestones using template
4. Track progress in dashboard

For Daily Updates

1. Create standup note: Ctrl+Shift+P → "Create Daily Standup"
2. Update active attack plans
3. Add progress to milestones
4. Capture any research notes

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Vault Version: 1.0.0
Last Updated: 2024-05-19
Maintained by: Research Stack Team

#obsidian-vault #knowledge-base #research-stack