feat: organize documentation into logical subdirectories

✅ Created organized project documentation structure
- project/ai-economics/: AI Economics Masters documentation
- project/cli/: Command-line interface documentation
- project/infrastructure/: System infrastructure and deployment docs
- project/requirements/: Project requirements and migration docs
- project/completion/: 100% project completion summary
- project/workspace/: Workspace strategy and organization

✅ Updated MASTER_INDEX.md to reflect new organization
- Added project documentation section with detailed breakdown
- Updated navigation to include new subdirectory structure
- Maintained existing documentation hierarchy

✅ Updated project/README.md for new organization
- Complete project documentation overview
- Directory structure explanation
- Quick access guide for each subdirectory
- Links to related documentation

📊 Documentation Organization Results:
- 10 files moved into 6 logical subdirectories
- Improved navigation and discoverability
- Maintained all existing content and links
- Enhanced project documentation structure

🎯 Documentation Status: 100% Organized and Complete

docs/project/infrastructure/RUNTIME_DIRECTORIES.md

@@ -0,0 +1,39 @@
+# AITBC Runtime Directory Structure
+
+This document outlines the standard Linux system directories used by AITBC for runtime data.
+
+## Standard System Directories
+
+### `/var/lib/aitbc/`
+**Purpose**: Application data and databases
+- `keystore/` - Blockchain private keys and certificates
+- `data/` - Application databases (.db, .sqlite files)
+- `logs/` - Application log files
+
+### `/etc/aitbc/`
+**Purpose**: Configuration files
+- Environment files (.env)
+- Service configuration
+- Network settings
+
+### `/var/log/aitbc/`
+**Purpose**: System logging (symlinked from `/var/lib/aitbc/logs/`)
+
+## Security & Permissions
+
+- **Keystore**: Restricted permissions (600/700)
+- **Config**: Read-only for services, writable for admin
+- **Logs**: Writable by services, readable by admin
+
+## Migration from Repo
+
+Runtime data has been moved from `/opt/aitbc/data/` to system standard directories:
+- Old: `/opt/aitbc/data/keystore/` → New: `/var/lib/aitbc/keystore/`
+- Old: `/opt/aitbc/data/` → New: `/var/lib/aitbc/data/`
+
+## SystemD Integration
+
+Services should be updated to use these standard paths:
+- `Environment=KEYSTORE_PATH=/var/lib/aitbc/keystore`
+- `Environment=DB_PATH=/var/lib/aitbc/data`
+- `Environment=LOG_PATH=/var/log/aitbc`