documentation to the root level docs

docs/DOCUMENTATION_MAP.md

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+# Documentation Map
+
+This document provides a comprehensive map of all documentation locations within the monorepo.
+
+## Root-Level Documentation
+
+### Project Documentation
+- **README.md** - Main project overview and quick start guide
+- **CONTRIBUTING.md** - Contribution guidelines
+- **SECURITY.md** - Security policies and reporting
+- **SETUP.md** - Detailed setup instructions
+- **CLAUDE.md** - Claude AI assistant guidelines
+- **PNPM_MIGRATION.md** - PNPM migration guide
+- **MAKEFILE_UPDATES.md** - Makefile usage and updates
+
+### Documentation Directories
+
+#### `/docs/`
+Project-wide documentation and guides
+
+- **automation notes/** - Automation and workflow documentation
+- **base skeleton version docs/** - Base architecture documentation
+- **MISP integration docs/** - MISP integration guides
+- **NX migration notes/** - NX workspace migration documentation
+- **apps/** - Application-specific documentation (organized by domain)
+
+#### `/specs/`
+Technical specifications and implementation plans
+
+- **spec.md** - Main specification document
+- **plan.md** - Project plan
+- **tasks.md** - Task tracking
+- **migration-strategy.md** - Migration strategy
+- **001-mental-prosthetic-platform/** - Platform specifications
+- Additional specification directories (002-xxx, 003-xxx, etc.)
+
+## Application Documentation
+
+All application-specific documentation has been centralized in `/docs/apps/` organized by domain:
+
+### Security Domain (`/docs/apps/security/`)
+
+| Application | Documentation Location | Key Contents |
+|------------|----------------------|--------------|
+| MISP | `security/misp/` | API docs, coding standards, security policies, roadmap |
+| Nemesis | `security/nemesis/` | Framework docs, NX integration guides |
+| YARA-X | `security/yara-x/` | Rule engine documentation |
+| KasmVNC | `security/kasmvnc/` | Building guides, debugging, RFB protocol specs |
+| APIScout | `security/apiscout/` | API analysis tool documentation |
+| Meterpreter | `security/meterpreter/` | Payload documentation |
+| HELK | `security/helk/` | Hunting ELK stack documentation |
+| BlackArch | `security/blackarch/` | Linux security tools documentation |
+| Dispatch | `security/dispatch/` | Incident management, plugin documentation |
+| Maltrail | `security/maltrail/` | Malware detection documentation |
+| CyberChef | `security/cyberchef/` | Data operations tool documentation |
+| Ghostwriter | `security/ghostwriter/` | Penetration testing reporting |
+| HexStrike | `security/hexstrike/` | AI-powered security tools |
+| Software Forensic Kit | `security/software-forensic-kit/` | Digital forensics documentation |
+| Security Service | `security/security-service/` | Domain aggregation service |
+
+### Productivity Domain (`/docs/apps/productivity/`)
+
+| Application | Documentation Location | Key Contents |
+|------------|----------------------|--------------|
+| Mealie | `productivity/mealie/` | Complete MkDocs site, contributor guides |
+| Goose | `productivity/goose/` | AI coding assistant documentation |
+| Onex | `productivity/onex/` | Exploitation toolkit documentation |
+| n8n | `productivity/n8n/` | Workflow automation, ESLint plugin, i18n, testing |
+
+### TCG Domain (`/docs/apps/tcg/`)
+
+| Application | Documentation Location | Key Contents |
+|------------|----------------------|--------------|
+| Commander Spellbook | `tcg/commander-spellbook/` | Backend API docs, frontend development guides |
+
+## Service README Files
+
+Each service maintains its own README.md in its application directory:
+
+### Security Services
+- `/apps/security/misp-service/README.md`
+- `/apps/security/nemesis-service/README.md`
+- `/apps/security/yara-x-service/README.md`
+- `/apps/security/kasmvnc-service/README.md`
+- `/apps/security/cyberchef-service/README.md`
+- `/apps/security/dispatch-service/README.md`
+- `/apps/security/ghostwriter-service/README.md`
+- `/apps/security/helk-service/README.md`
+- `/apps/security/maltrail-service/README.md`
+- And more...
+
+### Productivity Services
+- `/apps/productivity/mealie-service/README.md`
+- `/apps/productivity/n8n-service/README.md`
+- `/apps/productivity/actual-service/README.md`
+- `/apps/productivity/firecrawl-service/README.md`
+- `/apps/productivity/goose-service/README.md`
+- `/apps/productivity/inspector-service/README.md`
+- And more...
+
+### TCG Services
+- `/apps/tcg/commander-spellbook-backend/README.md`
+- `/apps/tcg/commander-spellbook-site/README.md`
+- `/apps/tcg/mtg-service/README.md`
+- And more...
+
+### Core Services
+- `/apps/core/jane-ui/README.md`
+- `/apps/core/jane-orchestrator/README.md`
+- `/apps/core/infrastructure-service/README.md`
+
+### AI Services
+- `/apps/ai/cyber-llm-server/README.md`
+- `/apps/ai/mtg-llm-server/README.md`
+- `/apps/ai/infrastructure-llm-server/README.md`
+
+## Library Documentation
+
+Libraries maintain their documentation within their respective directories:
+
+- `/libs/shared/` - Shared utilities and types
+- `/libs/ui/` - UI component library
+- `/libs/service-adapters/` - Service integration adapters
+- `/libs/firecrawl-core/` - Firecrawl core functionality
+- `/libs/mtg-scripting-toolkit/` - MTG scripting utilities
+- And more...
+
+## Development Documentation
+
+### Scripts
+- `/scripts/` - Build and utility scripts (many have inline documentation)
+
+### Infrastructure
+- `/infrastructure/docker/` - Docker configurations
+- `/infrastructure/kubernetes/` - Kubernetes manifests
+- `/infrastructure/terraform/` - Terraform IaC
+
+## Finding Documentation
+
+### By Topic
+
+**Getting Started**
+- Start with: `/README.md`
+- Setup: `/SETUP.md` or quick scripts: `setup-codespace.sh`, `quick-setup.sh`
+
+**Contributing**
+- Guide: `/CONTRIBUTING.md`
+- Code standards: Service-specific CODINGSTYLE.md in `/docs/apps/`
+
+**Security**
+- Policies: `/SECURITY.md`
+- Service-specific: `/docs/apps/security/<service>/SECURITY.md`
+
+**Architecture**
+- Specifications: `/specs/`
+- Base architecture: `/docs/base skeleton version docs/`
+
+**Service Usage**
+- Individual service READMEs in `/apps/<domain>/<service>/README.md`
+- Detailed docs in `/docs/apps/<domain>/<service>/`
+
+### By Format
+
+**Markdown Files**
+- Scattered throughout the repository
+- Primary locations: `/docs/`, `/specs/`, service directories
+
+**MkDocs Sites**
+- Mealie: `/docs/apps/productivity/mealie/docs/` (mkdocs.yml)
+
+**API Documentation**
+- MISP API: `/docs/apps/security/misp/api-docs/`
+- OpenAPI specs: Various service directories
+
+## Documentation Maintenance Guidelines
+
+1. **Service READMEs**: Keep in service root (`/apps/<domain>/<service>/README.md`)
+2. **Detailed Docs**: Extract to `/docs/apps/<domain>/<service>/`
+3. **Project Docs**: Keep in `/docs/` root
+4. **Specifications**: Keep in `/specs/`
+5. **Update This Map**: When adding new documentation locations
+
+## Quick Reference Commands
+
+```bash
+# Find all markdown files
+find . -name "*.md" -not -path "*/node_modules/*" -not -path "*/.venv/*"
+
+# Find documentation directories
+find . -type d -name "docs" -not -path "*/node_modules/*"
+
+# Search documentation content
+grep -r "search term" docs/ --include="*.md"
+```
+
+## Notes
+
+- Documentation has been **copied** (not moved) to preserve source integrity
+- Original documentation remains in service directories for backwards compatibility
+- `node_modules/` documentation has been excluded from centralization
+- API documentation and generated docs remain in their original locations

docs/DOCUMENTATION_MIGRATION_SUMMARY.md

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+# Documentation Migration Summary
+
+**Date**: November 15, 2025
+**Status**: Complete
+
+## Overview
+
+All application-specific documentation from the `apps/` directory has been centralized into `/docs/apps/`, organized by domain for easy discovery and maintenance.
+
+## Migration Actions
+
+### Documentation Copied
+Documentation was **copied** (not moved) to preserve source integrity and backwards compatibility.
+
+### Directory Structure Created
+
+```
+docs/apps/
+├── security/          # 15 security services documented
+├── productivity/      # 4 productivity services documented
+├── tcg/              # 1 TCG service documented
+├── core/             # (reserved for future core service docs)
+└── ai/               # (reserved for future AI service docs)
+```
+
+## Security Domain (15 Services)
+
+| Service | Documentation Copied | Location |
+|---------|---------------------|----------|
+| MISP | ✅ docs/, *.md, API docs | `/docs/apps/security/misp/` |
+| Nemesis | ✅ docs/, NX*.md | `/docs/apps/security/nemesis/` |
+| YARA-X | ✅ src/docs/, README-NX.md | `/docs/apps/security/yara-x/` |
+| KasmVNC | ✅ doc/, *.md | `/docs/apps/security/kasmvnc/` |
+| APIScout | ✅ docs/ | `/docs/apps/security/apiscout/` |
+| Meterpreter | ✅ docs/ | `/docs/apps/security/meterpreter/` |
+| HELK | ✅ assets/docs/ | `/docs/apps/security/helk/` |
+| BlackArch | ✅ blackarch/docs/ | `/docs/apps/security/blackarch/` |
+| Dispatch | ✅ plugin docs/, MIGRATION_SUMMARY.md | `/docs/apps/security/dispatch/` |
+| Maltrail | ✅ *.md files | `/docs/apps/security/maltrail/` |
+| CyberChef | ✅ *.md files | `/docs/apps/security/cyberchef/` |
+| Ghostwriter | ✅ *.md files | `/docs/apps/security/ghostwriter/` |
+| HexStrike | ✅ README_NX.md | `/docs/apps/security/hexstrike/` |
+| Software Forensic Kit | ✅ *.md files | `/docs/apps/security/software-forensic-kit/` |
+| Security Service | ✅ *.md files | `/docs/apps/security/security-service/` |
+
+## Productivity Domain (4 Services)
+
+| Service | Documentation Copied | Location |
+|---------|---------------------|----------|
+| Mealie | ✅ Complete docs/ (MkDocs site) | `/docs/apps/productivity/mealie/` |
+| Goose | ✅ docs/ | `/docs/apps/productivity/goose/` |
+| Onex | ✅ docs/ | `/docs/apps/productivity/onex/` |
+| n8n | ✅ Multiple package docs | `/docs/apps/productivity/n8n/` |
+
+## TCG Domain (1 Service)
+
+| Service | Documentation Copied | Location |
+|---------|---------------------|----------|
+| Commander Spellbook | ✅ backend docs/, frontend development-docs/ | `/docs/apps/tcg/commander-spellbook/` |
+
+## Files Created
+
+1. **`/docs/apps/README.md`**
+   - Comprehensive index of all application documentation
+   - Navigation guide by domain
+   - Maintenance guidelines
+
+2. **`/docs/DOCUMENTATION_MAP.md`**
+   - Complete documentation location reference
+   - Search strategies
+   - Quick reference commands
+
+3. **`/docs/DOCUMENTATION_MIGRATION_SUMMARY.md`** (this file)
+   - Migration summary and statistics
+
+## Key Statistics
+
+- **Total Services Documented**: 20
+- **Security Services**: 15
+- **Productivity Services**: 4
+- **TCG Services**: 1
+- **Documentation Directories Created**: 44
+- **Files Copied**: Hundreds of markdown files, images, and assets
+
+## What Was NOT Migrated
+
+- `node_modules/` documentation (excluded intentionally)
+- Individual service `README.md` files (kept in place)
+- Generated documentation (kept in source locations)
+- Build artifacts
+
+## Benefits
+
+### Before Migration
+- Documentation scattered across 37+ service directories
+- Difficult to discover available documentation
+- No central index or navigation
+- Mixed with source code
+
+### After Migration
+- Centralized documentation hub at `/docs/apps/`
+- Clear domain-based organization
+- Comprehensive index and map
+- Easy discovery and maintenance
+- Original sources preserved
+
+## Access Patterns
+
+### Find Documentation by Service
+1. Navigate to `/docs/apps/`
+2. Choose domain: `security/`, `productivity/`, or `tcg/`
+3. Find service directory
+4. Browse documentation
+
+### Find Documentation by Topic
+1. Check `/docs/DOCUMENTATION_MAP.md` for topic index
+2. Use table of contents in `/docs/apps/README.md`
+3. Search using grep: `grep -r "topic" docs/apps/ --include="*.md"`
+
+## Maintenance Going Forward
+
+### When Adding a New Service
+1. Create service in appropriate domain: `/apps/<domain>/<service>/`
+2. Keep README.md in service root
+3. Copy detailed docs to: `/docs/apps/<domain>/<service>/`
+4. Update `/docs/apps/README.md` index
+5. Update `/docs/DOCUMENTATION_MAP.md` if needed
+
+### When Updating Documentation
+1. Update source documentation in service directory
+2. Copy updates to `/docs/apps/<domain>/<service>/`
+3. Keep both locations in sync
+
+## Related Documentation
+
+- **Main README**: `/README.md` - Project overview
+- **Setup Guide**: `/SETUP.md` - Installation and configuration
+- **Specifications**: `/specs/` - Technical specifications
+- **Base Documentation**: `/docs/base skeleton version docs/` - Architecture docs
+
+## Migration Script
+
+The migration was performed using a bash script that:
+1. Created organized directory structure
+2. Copied documentation preserving hierarchy
+3. Handled special cases (plugins, nested docs, etc.)
+4. Excluded node_modules and build artifacts
+
+Script preserved at: `/tmp/move_docs.sh`
+
+## Validation
+
+To verify the migration:
+
+```bash
+# Check directory structure
+tree -L 3 -d /workspaces/modular-monolith-2/docs/apps/
+
+# Count documentation directories
+find /workspaces/modular-monolith-2/docs/apps/ -type d | wc -l
+
+# Find all markdown files
+find /workspaces/modular-monolith-2/docs/apps/ -name "*.md" | wc -l
+```
+
+## Next Steps
+
+1. ✅ Documentation centralized
+2. ✅ Index and map created
+3. ⏳ Consider automating sync between source and docs/apps/
+4. ⏳ Add documentation to CI/CD pipeline
+5. ⏳ Create documentation site (MkDocs, Docusaurus, etc.)
+6. ⏳ Add search functionality
+
+## Notes
+
+- Original documentation remains in service directories (backwards compatibility)
+- Both locations should be kept in sync when updating
+- Consider creating symbolic links or automation for future sync
+- MkDocs site could aggregate all documentation