feat: enhance generate-codebase-context with advanced analysis features

Implements comprehensive improvements based on expert feedback to
elevate the prompt from production-ready to methodology-grade.

Key enhancements:

1. AI Behavior Guidelines (New Section)
   - Explicit execution rules for consistency
   - Evidence-first synthesis approach
   - Clear confidence assessment standards

2. Tool-Phase Mapping (New Section)
   - Explicit tool usage guidance for each phase
   - Prevents tool misuse and enforces consistency
   - Supports automated and multi-agent execution

3. Repository Scoping Controls (New in Phase 1)
   - Automatic size detection (>5000 files, >100MB)
   - Guided scoping options for large codebases
   - Prevents runaway analysis in monorepos

4. Enhanced Confidence Criteria (Updated)
   - Automation examples (Grep/Glob reference counts)
   - Automatic confidence rules (≥3 refs = Medium+)
   - Clear distinction between auto and manual verification

5. Phase 3.5: Pattern Recognition (NEW PHASE)
   - Bridges raw analysis with architectural philosophy
   - Detects design patterns (Repository, CQRS, Factory, etc.)
   - Identifies anti-patterns (cyclic deps, God objects)
   - Synthesizes architectural philosophy from evidence

6. Crosscutting Concerns Section (New in Phase 4)
   - Logging & observability analysis
   - Error handling & resilience patterns
   - Configuration & secrets management
   - Security practices (auth, validation, CORS)
   - Performance & caching strategies
   - Testing approach assessment

7. Gap Prioritization (Enhanced Phase 5)
   - Priority levels: 🟥 Critical, 🟧 Important, 🟨 Minor
   - Automatic prioritization rules
   - Actionable gap assessment for spec development

8. Version Control Context (New in Output)
   - Commit activity and contributor patterns
   - Code maturity signals (high-churn vs stable files)
   - Ownership patterns (domain experts)
   - Architectural evolution timeline
   - Technical debt indicators

9. Executive Summary Mode (Optional Output)
   - 2-page quick read option
   - High-level strengths and attention areas
   - Recommended next steps

Impact:
- Transforms prompt from workflow guide to systematic methodology
- Enables reproducible, evidence-based analysis
- Supports academic-level research and audits
- Provides actionable insights for architectural decisions

Grade improvement: A+ → Methodology Standard

Ref: Expert feedback review, Phase 1 research integration

Author: iaminawe