agentic-sdlc 1.0.0 → 1.5.0

package/docs/PROJECT-DOCUMENTATION-INDEX.md

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+# Project Documentation Index
+
+**Last Updated:** 2026-01-01  
+**Status:** Current
+
+This document provides a complete index of all project documentation after the reorganization and file naming standardization.
+
+---
+
+## 📋 Quick Reference
+
+### Getting Started
+- [README.md](../README.md) - Project overview
+- [QUICK-START.md](guides/QUICK-START.md) - Quick start guide
+- [INTEGRATION-GUIDE.md](guides/INTEGRATION-GUIDE.md) - Integration guide
+
+### Project Structure
+- [PROJECT-STRUCTURE.md](../PROJECT-STRUCTURE.md) - Detailed structure
+- [STRUCTURE.md](../STRUCTURE.md) - Structure overview
+- [REORGANIZATION-COMPLETE.md](../REORGANIZATION-COMPLETE.md) - Reorganization details
+- [FILE-NAMING-COMPLETE.md](../FILE-NAMING-COMPLETE.md) - Naming standards
+- [STANDARDIZATION-SUMMARY.md](../STANDARDIZATION-SUMMARY.md) - Complete summary
+
+### Setup & Configuration
+- [RESEARCH-AGENT-SETUP.md](setup/RESEARCH-AGENT-SETUP.md) - Research agent setup
+- [GITHUB-MANAGEMENT.md](setup/GITHUB-MANAGEMENT.md) - GitHub integration
+- [MCP-SETUP.md](guides/MCP-SETUP.md) - MCP configuration
+
+---
+
+## 📁 Documentation by Category
+
+### 1. Root Documentation
+
+**Location:** `/`
+
+| File | Description | Status |
+|------|-------------|--------|
+| `README.md` | Main project documentation | ✅ Current |
+| `CHANGELOG.md` | Version history | ✅ Current |
+| `PROJECT-STRUCTURE.md` | Project structure details | ✅ Current |
+| `STRUCTURE.md` | Structure overview | ✅ Current |
+| `REORGANIZATION-COMPLETE.md` | File reorganization summary | ✅ Current |
+| `FILE-NAMING-STANDARDS.md` | Naming convention rules | ✅ Current |
+| `FILE-NAMING-COMPLETE.md` | Naming standardization details | ✅ Current |
+| `STANDARDIZATION-SUMMARY.md` | Complete standardization summary | ✅ Current |
+
+---
+
+### 2. Agent Framework Documentation
+
+**Location:** `.agent/`
+
+#### Core Documentation
+| File | Description | Path |
+|------|-------------|------|
+| `USAGE.md` | Agent usage guide | `.agent/USAGE.md` |
+
+#### IDE Integration
+**Location:** `.agent/ide-integration/`
+
+| File | Description | Status |
+|------|-------------|--------|
+| `README.md` | IDE integration overview | ✅ Current |
+| `AIDER-COMMANDS.md` | Aider AI commands | ✅ Current |
+| `CURSOR-RULES.md` | Cursor IDE rules | ✅ Current |
+| `GITHUB-COPILOT-INSTRUCTIONS.md` | GitHub Copilot setup | ✅ Current |
+| `WINDSURF-CASCADE.md` | Windsurf Cascade config | ✅ Current |
+| `cline-config.json` | Cline configuration | ✅ Current |
+| `vscode-commands.json` | VS Code commands | ✅ Current |
+
+#### Knowledge Base
+**Location:** `.agent/knowledge-base/`
+
+| File | Description | Status |
+|------|-------------|--------|
+| `README.md` | Knowledge base overview | ✅ Current |
+| `INDEX.md` | Knowledge base index | ✅ Current |
+| `AUTO-LEARNING-GUIDE.md` | Auto-learning guide | ✅ Current |
+
+**Categories:**
+- `architecture/` - Architecture decisions
+- `bugs/` - Bug fixes and solutions
+- `features/` - Feature implementations
+- `performance/` - Performance optimizations
+- `security/` - Security fixes
+- `platform-specific/` - Platform-specific solutions
+- `role-guides/` - Role-specific guides
+
+#### Rules
+**Location:** `.agent/rules/`
+
+| File | Description | Status |
+|------|-------------|--------|
+| `GLOBAL.md` | Global rules | ✅ Current |
+| `ARTIFACTS.md` | Artifact rules | ✅ Current |
+| `AUTO-LEARNING.md` | Auto-learning rules | ✅ Current |
+| `GIT-WORKFLOW.md` | Git workflow rules | ✅ Current |
+| `KNOWLEDGE-BASE.md` | Knowledge base rules | ✅ Current |
+
+#### Templates
+**Location:** `.agent/templates/`
+
+All 16 template files follow the pattern: `Word-Word-Template.md`
+
+| Template | Purpose |
+|----------|---------|
+| `Project-Plan-Template.md` | Project planning |
+| `Product-Backlog-Template.md` | Product backlog |
+| `System-Design-Spec-Template.md` | System design |
+| `UIUX-Design-Spec-Template.md` | UI/UX design |
+| `Design-Verification-Report-Template.md` | Design verification |
+| `Security-Review-Report-Template.md` | Security review |
+| `Development-Log-Template.md` | Development logs |
+| `DevOps-Plan-Template.md` | DevOps planning |
+| `Test-Report-Template.md` | Testing reports |
+| `Final-Project-Report-Template.md` | Final reports |
+| `Final-Approval-Report-Template.md` | Final approval |
+| `Phase-Report-Template.md` | Phase reports |
+| `Master-Documentation-Template.md` | Master docs |
+| `Knowledge-Entry-Template.md` | Knowledge entries |
+| `CHANGELOG-Template.md` | Changelog |
+| `definition-of-done.md` | Definition of done |
+| `incident-response.md` | Incident response |
+
+#### Workflows
+**Location:** `.agent/workflows/`
+
+All 18 workflow files use lowercase naming.
+
+| Workflow | Description |
+|----------|-------------|
+| `pm.md` | Project Manager |
+| `po.md` | Product Owner |
+| `sa.md` | System Analyst |
+| `uiux.md` | UI/UX Designer |
+| `qa.md` | Quality Assurance |
+| `seca.md` | Security Analyst |
+| `dev.md` | Developer |
+| `devops.md` | DevOps Engineer |
+| `tester.md` | Tester |
+| `reporter.md` | Reporter |
+| `stakeholder.md` | Stakeholder |
+| `auto.md` | Automation |
+| `research.md` | Research workflow |
+| `brain.md` | Brain/AI workflow |
+| `auto-learning-workflow.md` | Auto-learning |
+| `git-kb-integration.md` | Git KB integration |
+| `kb-hooks-setup.md` | KB hooks setup |
+| `kb-search.md` | KB search |
+
+---
+
+### 3. Configuration Documentation
+
+#### Kiro Steering Files
+**Location:** `.kiro/steering/`
+
+All 17 steering files use lowercase naming.
+
+| File | Description |
+|------|-------------|
+| `README.md` | Steering overview |
+| `00-teamlifecycle-overview.md` | TeamLifecycle overview |
+| `global-rules.md` | Global rules |
+| `git-workflow.md` | Git workflow |
+| `knowledge-base.md` | Knowledge base management |
+| `role-pm.md` | PM role |
+| `role-po.md` | PO role |
+| `role-sa.md` | SA role |
+| `role-uiux.md` | UI/UX role |
+| `role-qa.md` | QA role |
+| `role-seca.md` | Security role |
+| `role-dev.md` | Developer role |
+| `role-devops.md` | DevOps role |
+| `role-tester.md` | Tester role |
+| `role-reporter.md` | Reporter role |
+| `role-stakeholder.md` | Stakeholder role |
+| `role-orchestrator.md` | Orchestrator role |
+
+#### GitHub Configuration
+**Location:** `.github/`
+
+| File | Description | Status |
+|------|-------------|--------|
+| `COPILOT-INSTRUCTIONS.md` | Copilot instructions | ✅ Current |
+
+**Issue Templates:** `.github/ISSUE_TEMPLATE/`
+- `bug_report.yml`
+- `feature_request.yml`
+- `security_alert.yml`
+- `task_implementation.yml`
+- `config.yml`
+
+---
+
+### 4. Project Documentation
+
+**Location:** `docs/`
+
+#### Main Documentation
+| File | Description | Status |
+|------|-------------|--------|
+| `OUTLINE.md` | Documentation outline | ✅ Current |
+| `PROJECT-DOCUMENTATION-INDEX.md` | This file | ✅ Current |
+| `SDLC-Diagram.md` | SDLC workflow diagrams | ✅ Current |
+| `BRAIN-ARCHITECTURE.md` | BRAIN orchestrator architecture | ✅ Current |
+| `ARCHITECTURE-OVERVIEW.md` | Complete system architecture | ✅ Current |
+| `KNOWLEDGE-BASE-GUIDE.md` | KB visual guide with diagrams | ✅ Current |
+| `KNOWLEDGE-BASE-SIMPLE.md` | KB quick reference | ✅ Current |
+| `NEO4J-COMPOUND-INTEGRATION.md` | Neo4j integration guide | ✅ Current |
+| `NEO4J-INTEGRATION-COMPLETE.md` | Neo4j implementation summary | ✅ Current |
+| `NEO4J-DOCS-INTEGRATION-COMPLETE.md` | Neo4j + docs/ integration | ✅ Current |
+| `CLI-REORGANIZATION-COMPLETE.md` | Cross-platform CLI reorganization | ✅ Current |
+| `CLI-TESTING-RESULTS.md` | CLI testing results (Windows) | ✅ Current |
+
+#### Architecture
+**Location:** `docs/architecture/`
+
+| File | Description | Status |
+|------|-------------|--------|
+| `BRAIN.md` | Brain architecture | ✅ Current |
+| `NEO4J-LEARNING-QUERIES.md` | Neo4j queries | ✅ Current |
+
+#### Guides
+**Location:** `docs/guides/`
+
+All guide files use UPPERCASE naming.
+
+| File | Description | Status |
+|------|-------------|--------|
+| `QUICK-START.md` | Quick start guide | ✅ Current |
+| `CLI-EXAMPLES.md` | CLI examples | ✅ Current |
+| `INTEGRATION-GUIDE.md` | Integration guide | ✅ Current |
+| `AUTO-LEARNING-SYSTEM.md` | Auto-learning system | ✅ Current |
+| `AUTO-LEARNING-COMPLETE-GUIDE.md` | Complete auto-learning | ✅ Current |
+| `LEARNING-FLOW.md` | Learning flow | ✅ Current |
+| `MCP-GUIDE.md` | MCP guide | ✅ Current |
+| `MCP-QUICK-REFERENCE.md` | MCP quick reference | ✅ Current |
+| `MCP-SETUP.md` | MCP setup | ✅ Current |
+| `ROLE-COMMUNICATION-SYSTEM.md` | Role chat system guide | ✅ Current |
+
+#### Reports
+**Location:** `docs/reports/`
+
+| File | Description | Status |
+|------|-------------|--------|
+| `COMPARISON-LEANN-NEO4J.md` | LeANN vs Neo4j comparison | ✅ Current |
+| `UIUX-Design-Skills-Research-Report-2026.md` | UI/UX research | ✅ Current |
+
+#### Setup
+**Location:** `docs/setup/`
+
+| File | Description | Status |
+|------|-------------|--------|
+| `RESEARCH-AGENT-SETUP.md` | Research agent setup | ✅ Current |
+| `GITHUB-MANAGEMENT.md` | GitHub management | ✅ Current |
+
+#### Sprints
+**Location:** `docs/sprints/`
+
+| File | Description | Status |
+|------|-------------|--------|
+| `SPRINT-GITHUB-ISSUES.md` | GitHub issues sprint | ✅ Current |
+| `SPRINT-LEANN-INTEGRATION.md` | LeANN integration sprint | ✅ Current |
+| `SPRINT-NEO4J-BRAIN.md` | Neo4j brain sprint | ✅ Current |
+
+**Sprint Directories:**
+- `sprint-1/` - First sprint artifacts
+- `sprint-2/` - Second sprint artifacts
+
+#### Research Reports
+**Location:** `docs/research-reports/`
+
+Generated research reports (JSON and Markdown format).
+
+---
+
+### 5. Tools Documentation
+
+**Location:** `tools/`
+
+#### Research Agent
+**Location:** `tools/research/`
+
+| File | Description | Status |
+|------|-------------|--------|
+| `README.md` | Research agent documentation | ✅ Current |
+| `research_agent.py` | Core research agent | ✅ Current |
+| `research_mcp.py` | MCP integration | ✅ Current |
+| `research_mcp_extended.py` | Extended MCP | ✅ Current |
+
+**Usage:**
+```bash
+python tools/research/research_agent.py --task "..." --type feature
+```
+
+#### Neo4j Tools
+**Location:** `tools/neo4j/`
+
+| File | Description | Status |
+|------|-------------|--------|
+| `README.md` | Neo4j documentation | ✅ Current |
+| `graph_brain.py` | Graph brain | ✅ Current |
+| `sync_skills_to_neo4j.py` | Skills sync | ✅ Current |
+| `query_skills_neo4j.py` | Skills query | ✅ Current |
+| `test_neo4j_connection.py` | Connection test | ✅ Current |
+| `verify_neo4j.py` | Verification | ✅ Current |
+| `requirements.txt` | Dependencies | ✅ Current |
+
+**Usage:**
+```bash
+python tools/neo4j/sync_skills_to_neo4j.py
+python tools/neo4j/query_skills_neo4j.py --all-skills
+```
+
+#### GitHub Tools
+**Location:** `tools/github/`
+
+| File | Description | Status |
+|------|-------------|--------|
+| `sync_github.py` | GitHub sync | ✅ Current |
+
+#### Setup Scripts
+**Location:** `tools/setup/`
+
+| File | Description | Status |
+|------|-------------|--------|
+| `setup_research_hooks.sh` | Research hooks setup | ✅ Current |
+| `standardize_filenames.ps1` | File naming script | ✅ Current |
+
+---
+
+## 🔍 Finding Documentation
+
+### By Topic
+
+**Getting Started:**
+- Quick Start: `docs/guides/QUICK-START.md`
+- Integration: `docs/guides/INTEGRATION-GUIDE.md`
+- CLI Examples: `docs/guides/CLI-EXAMPLES.md`
+
+**Research Agent:**
+- Setup: `docs/setup/RESEARCH-AGENT-SETUP.md`
+- Documentation: `tools/research/README.md`
+- Workflow: `.agent/workflows/research.md`
+
+**Neo4j:**
+- Integration Guide: `docs/NEO4J-COMPOUND-INTEGRATION.md`
+- Implementation Summary: `docs/NEO4J-INTEGRATION-COMPLETE.md`
+- Documentation: `tools/neo4j/README.md`
+- Architecture: `docs/architecture/BRAIN.md`
+- Queries: `docs/architecture/NEO4J-LEARNING-QUERIES.md`
+
+**Knowledge Base:**
+- Overview: `.agent/knowledge-base/README.md`
+- Visual Guide: `docs/KNOWLEDGE-BASE-GUIDE.md`
+- Quick Reference: `docs/KNOWLEDGE-BASE-SIMPLE.md`
+- Rules: `.agent/rules/KNOWLEDGE-BASE.md`
+- Auto-Learning: `.agent/knowledge-base/AUTO-LEARNING-GUIDE.md`
+- Scripts: `bin/README.md`
+
+**MCP Integration:**
+- Guide: `docs/guides/MCP-GUIDE.md`
+- Setup: `docs/guides/MCP-SETUP.md`
+- Quick Reference: `docs/guides/MCP-QUICK-REFERENCE.md`
+
+**Workflows:**
+- All workflows: `.agent/workflows/`
+- Steering files: `.kiro/steering/`
+
+### By File Type
+
+**UPPERCASE Documentation (WORD-WORD.md):**
+- All guides in `docs/guides/`
+- All reports in `docs/reports/`
+- All setup docs in `docs/setup/`
+- All architecture docs in `docs/architecture/`
+- All sprint docs in `docs/sprints/`
+- All rules in `.agent/rules/`
+- All IDE integration in `.agent/ide-integration/`
+
+**lowercase files (word.md, word-word.md):**
+- All workflows in `.agent/workflows/`
+- All steering files in `.kiro/steering/`
+
+**Title-Case-Template.md:**
+- All templates in `.agent/templates/`
+
+**lowercase_with_underscores.py:**
+- All Python scripts in `tools/`
+
+---
+
+## 📊 Documentation Statistics
+
+### Total Files
+- **Root Documentation:** 8 files
+- **Agent Framework:** 50+ files
+- **Configuration:** 20+ files
+- **Project Documentation:** 30+ files
+- **Tools Documentation:** 10+ files
+
+### By Category
+- **Guides:** 9 files
+- **Templates:** 16 files
+- **Workflows:** 18 files
+- **Steering Files:** 17 files
+- **Rules:** 5 files
+- **Tools:** 10+ scripts
+
+### File Naming
+- **UPPERCASE:** 40+ documentation files
+- **lowercase:** 35+ workflow/steering files
+- **Title-Case:** 16 template files
+- **lowercase_underscore:** 10+ Python scripts
+
+---
+
+## 🔄 Recent Changes
+
+### 2026-01-02: docs/ Directory Integration with Neo4j Brain
+1. **Knowledge Base Expansion**
+   - Integrated `docs/` directory into KB system
+   - Increased indexed entries from 6 to 46 (7x increase)
+   - All documentation now searchable via KB CLI
+   - Neo4j Brain now indexes all project documentation
+
+2. **Updated Modules**
+   - `bin/lib/kb_common.py` - Added docs path support
+   - `bin/lib/kb_search.py` - Search both KB + docs
+   - `bin/lib/kb_index.py` - Index both locations
+   - `bin/lib/kb_compound.py` - Compound ops for both
+   - `tools/neo4j/sync_skills_to_neo4j.py` - Sync both locations
+
+3. **Documentation**
+   - Created `NEO4J-DOCS-INTEGRATION-COMPLETE.md`
+   - Updated all KB documentation
+   - Added comprehensive testing results
+
+### 2026-01-02: Cross-Platform CLI Reorganization
+1. **Python-Based CLI**
+   - Replaced PowerShell scripts with Python
+   - Created unified CLI for Windows/Linux/macOS
+   - 5-10x faster performance
+   - Better error handling and ANSI colors
+
+2. **New Structure**
+   - `bin/kb` (bash entry point)
+   - `bin/kb.bat` (Windows batch entry)
+   - `bin/kb_cli.py` (Python CLI)
+   - `bin/lib/*.py` (7 library modules)
+
+3. **Documentation**
+   - Created `CLI-REORGANIZATION-COMPLETE.md`
+   - Created `CLI-TESTING-RESULTS.md`
+   - Updated `bin/README.md`
+
+### 2026-01-02: Neo4j Compound Integration
+1. **Neo4j Brain Integration**
+   - Created compound script system (`kb-compound.ps1`)
+   - Integrated Neo4j as knowledge graph brain
+   - Implemented hybrid file + graph storage
+   - Added compound commands (search, add, sync, query, stats)
+
+2. **Documentation**
+   - Created `NEO4J-COMPOUND-INTEGRATION.md` (complete guide)
+   - Created `NEO4J-INTEGRATION-COMPLETE.md` (summary)
+   - Updated `bin/README.md` with compound commands
+   - Updated `.agent/knowledge-base/README.md`
+
+3. **Scripts**
+   - Created `kb-compound.ps1` (compound operations)
+   - Updated `kb.ps1` (added compound mode)
+   - Fixed `kb-stats.ps1` (syntax error)
+   - Verified Neo4j sync and query scripts
+
+### 2026-01-01: Major Reorganization
+1. **File Reorganization**
+   - Moved research tools to `tools/research/`
+   - Moved Neo4j tools to `tools/neo4j/`
+   - Moved GitHub tools to `tools/github/`
+   - Moved setup scripts to `tools/setup/`
+
+2. **File Naming Standardization**
+   - Renamed 17 files to UPPERCASE
+   - Applied consistent naming conventions
+   - Ensured 100% English names
+
+3. **Documentation Updates**
+   - Updated all path references
+   - Created comprehensive indexes
+   - Added this documentation index
+
+---
+
+## 📝 Contributing
+
+### Adding New Documentation
+
+**Documentation Files:**
+```bash
+# Use UPPERCASE-WITH-HYPHENS.md
+docs/guides/NEW-GUIDE.md
+```
+
+**Workflow Files:**
+```bash
+# Use lowercase.md or lowercase-with-hyphens.md
+.agent/workflows/new-workflow.md
+```
+
+**Template Files:**
+```bash
+# Use Title-Case-Template.md
+.agent/templates/New-Template.md
+```
+
+### Updating Documentation
+
+1. Follow naming conventions in `FILE-NAMING-STANDARDS.md`
+2. Update this index when adding new files
+3. Keep cross-references current
+4. Use relative paths for links
+
+---
+
+## 🔗 External Resources
+
+- **Neo4j Browser:** https://workspace-preview.neo4j.io/workspace/query
+- **GitHub Repository:** (configured in `.env`)
+- **Landing Page:** `landing-page/` directory
+
+---
+
+**Last Updated:** 2026-01-02  
+**Maintained By:** Agentic SDLC Team  
+**Status:** ✅ Current and Complete
+
+**Latest:** Neo4j compound integration complete with hybrid file + graph storage system.