feat: complete comprehensive capability inclusion management system

Implement revolutionary capability inclusion management system with complete
documentation ecosystem and automated discovery tools to prevent code duplication
and ensure proper separation of concerns.

Key accomplishments:
- Comprehensive capability documentation ecosystem (5 interconnected files)
- Clear separation: internal capabilities (what MarkiTect provides) vs external capabilities (what MarkiTect uses)
- Automated discovery tools preventing code duplication (make capability-search)
- AI-assistant optimized workflow with quick reference guide
- Enhanced project-assistant agent definition with capability inclusion workflow
- Updated README.md with clear links to capability documentation
- Complete session wrap-up with updated ProjectDiary.md, NEXT.md, and ProjectStatusDigest.md

Architecture milestone: Establishes MarkiTect as mature project with enterprise-grade
capability management, transforming development from ad-hoc implementation to
systematic capability management with automated duplication prevention.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

CAPABILITIES.md

@@ -1,14 +1,18 @@
-# MarkiTect System Capabilities & Extraction Plan
+# MarkiTect Internal Capabilities Inventory
 
-> **Comprehensive overview of all capabilities, architectural innovations, and capability extraction recommendations for the ComposableRepositoryParadigm**
+> **Comprehensive overview of all capabilities PROVIDED BY MarkiTect - what this repository offers to the world**
 
 ## Overview
 
-- **Total Capabilities**: 73+ distinct capabilities
+This document catalogs all **internal capabilities** that MarkiTect provides - the functionality that this repository offers to users and other projects. These are capabilities that MarkiTect **provides**, not **uses**.
+
+- **Total Internal Capabilities**: 73+ distinct capabilities
 - **Test Categories**: 15 major functional areas
 - **Test Coverage**: 348 tests across 27 test files
 - **Architecture**: Database-driven system with AST-based markdown processing, multi-layer caching, and deep Git platform integration
-- **Extraction Status**: 2 capabilities extracted, 11 candidates identified for extraction
+- **Extraction Status**: 2 capabilities extracted to external, 11 candidates identified for extraction
+
+> **Note**: For capabilities that MarkiTect **uses** (external dependencies), see `CAPABILITY_REGISTRY.md`. For complete architecture understanding, see `CAPABILITY_INCLUSION_GUIDE.md`.
 
 ---