test: Add Mermaid parser validation and enhance stateDiagram support

- Enhanced MermaidParser with stateDiagram-v2 detection and parsing
- Added _parse_state_diagram() method for state transitions and labels
- Created comprehensive test suite (test/manual/test_mermaid_parser.py)
- All 13 architecture diagrams validated (100% pass rate)
- Generated detailed test report (547 elements, 503 relationships parsed)
- Archived old diagram files to doc/design/diagrams-old/
- Organized test artifacts into proper test/ directory structure

Author: vinod0m

ARCHIVE_REORGANIZATION_SUMMARY.md

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+# Documentation Archive Reorganization - Summary
+
+**Date:** October 7, 2025  
+**Branch:** dev/PrV-unstructuredData-extraction-docling  
+**Commits:** 2 (5d5f371, 8c65681)
+
+---
+
+## Overview
+
+Successfully reorganized all working documents from previous phases and tasks into a well-structured archive system within `doc/.archive/`, while ensuring all relevant information has been integrated into current documentation.
+
+## What Was Accomplished
+
+### 1. DocumentAgent Quality Enhancements Integrated (Commit 5d5f371)
+
+**Problem Identified:**
+- System architecture description didn't fit current code status
+- DocumentAgent quality enhancements (99-100% accuracy) were missing from codeDoc
+- User had manually edited 7 files indicating dissatisfaction with generated content
+
+**Solution Implemented:**
+
+Updated 4 key documentation files with comprehensive quality enhancement details:
+
+#### doc/codeDocs/agents.rst
+- ✅ Added comprehensive DocumentAgent section with 99-100% accuracy features
+- ✅ Documented 6 quality components with accuracy contributions
+- ✅ Added quality metrics: avg confidence 0.965, auto-approve 100%
+- ✅ Included usage examples and method descriptions
+- ✅ Listed all 25 methods including quality enhancement methods
+
+#### doc/codeDocs/prompt_engineering.rst
+- ✅ Documented RequirementsPromptLibrary (doc-type prompts, +2%)
+- ✅ Documented FewShotManager (domain examples, +2-3%)
+- ✅ Documented ExtractionInstructionsLibrary (enhanced instructions, +3-5%)
+- ✅ Added integration pipeline diagram showing component flow
+- ✅ Included code examples for each library
+
+#### doc/codeDocs/pipelines.rst
+- ✅ Documented EnhancedOutputBuilder with confidence scoring
+- ✅ Added ConfidenceLevel enumeration (HIGH/MEDIUM/LOW)
+- ✅ Documented quality flag detection (PII, duplicates, completeness)
+- ✅ Documented MultiStageExtractor (+1-2% accuracy)
+- ✅ Included usage examples and quality metrics
+
+#### doc/codeDocs/overview.rst
+- ✅ Replaced generic description with accurate 5-layer architecture
+- ✅ Added detailed DocumentAgent Quality Enhancement Pipeline diagram
+- ✅ Documented quality metrics and component contributions
+- ✅ Aligned with README architecture (22 modules, 5 layers)
+- ✅ Added comprehensive data flow diagram
+
+### 2. Working Documents Archived (Commit 8c65681)
+
+**Problem Identified:**
+- 16 working documents from previous phases cluttering doc/ folder
+- PHASE2_TASK*, PHASE*_COMPLETE, TASK*_SUMMARY, ADVANCED_TAGGING*, etc.
+- Information not properly maintained in new documentation structure
+
+**Solution Implemented:**
+
+Created 3 organized archive folders with comprehensive README files:
+
+#### Archive: phase2-task6/ (Performance Optimization)
+**Files Archived:**
+- PHASE2_TASK6_FINAL_REPORT.md - Complete benchmarking methodology
+- TASK6_COMPLETION_SUMMARY.md - Executive summary
+
+**Key Achievement:** 93% accuracy with 5:1 chunk-to-token ratio  
+**Optimal Config:** 4000/800/800 (chunk_size/overlap/max_tokens)  
+**Integration:** User-guide/configuration.md, developer-guide/development-setup.md
+
+#### Archive: phase2-task7/ (Prompt Engineering)
+**Files Archived (10 total):**
+- PHASE2_TASK7_PLAN.md - Overall implementation plan
+- PHASE2_TASK7_PHASE1_ANALYSIS.md - Missing requirements analysis
+- PHASE2_TASK7_PHASE2_PROMPTS.md - Document-specific prompts
+- PHASE2_TASK7_PHASE3_FEW_SHOT.md - Few-shot learning
+- PHASE2_TASK7_PHASE4_INSTRUCTIONS.md - Enhanced instructions
+- PHASE2_TASK7_PHASE5_MULTISTAGE.md - Multi-stage extraction
+- PHASE2_TASK7_PROGRESS.md - Progress tracking
+- PHASE4_COMPLETE.md - Phase 4 completion
+- PHASE5_COMPLETE.md - Phase 5 completion
+- TASK7_TAGGING_ENHANCEMENT.md - Tagging enhancements
+
+**Key Achievement:** 93% → 99-100% accuracy (6-7% improvement)  
+**Components:** 5 quality enhancement phases  
+**Integration:** codeDocs/agents.rst, prompt_engineering.rst, pipelines.rst, overview.rst
+
+#### Archive: advanced-tagging/ (ML-Based Tagging)
+**Files Archived:**
+- ADVANCED_TAGGING_ENHANCEMENTS.md - ML classification features
+- DOCUMENT_TAGGING_SYSTEM.md - Core architecture
+- IMPLEMENTATION_SUMMARY_ADVANCED_TAGGING.md - Implementation details
+- INTEGRATION_GUIDE.md - Integration instructions
+
+**Key Achievement:** 95%+ tag accuracy with hybrid ML+rule-based approach  
+**Features:** Multi-label classification, tag hierarchies, A/B testing, custom tags  
+**Integration:** features/document-tagging.md, developer-guide/architecture.md
+
+### 3. Documentation Structure Updated
+
+**doc/.archive/README.md:**
+- ✅ Added phase2-task6 section with optimal config summary
+- ✅ Added phase2-task7 section with quality enhancement details
+- ✅ Added advanced-tagging section with ML features
+- ✅ Updated archive organization overview
+
+**doc/README.md:**
+- ✅ Updated historical documentation section
+- ✅ Added references to 3 new archive folders
+- ✅ Noted 60+ working docs properly archived
+- ✅ Added archive navigation notes
+
+---
+
+## Files Summary
+
+### Commit 5d5f371: Quality Enhancement Documentation
+**Files Modified:** 4
+- doc/codeDocs/agents.rst (576 lines added)
+- doc/codeDocs/prompt_engineering.rst (enhanced with quality libs)
+- doc/codeDocs/pipelines.rst (enhanced output structure)
+- doc/codeDocs/overview.rst (accurate architecture)
+
+**Lines Changed:** ~600+ additions, ~120 deletions
+
+### Commit 8c65681: Archive Reorganization
+**Files Moved:** 16 working documents  
+**Archive READMEs Created:** 3  
+**Total Files Changed:** 21  
+**Lines Added:** 363  
+
+### Combined Impact
+**Total Commits:** 2  
+**Total Files Changed:** 25  
+**Working Docs Archived:** 16  
+**New Archive Folders:** 3  
+**Documentation Updated:** 6 files  
+
+---
+
+## Integration Status
+
+### ✅ Fully Integrated Components
+
+**DocumentAgent Quality Enhancements:**
+- Code Documentation: doc/codeDocs/agents.rst (comprehensive)
+- Prompt Engineering: doc/codeDocs/prompt_engineering.rst (3 libraries documented)
+- Pipelines: doc/codeDocs/pipelines.rst (EnhancedOutputBuilder, MultiStageExtractor)
+- Architecture: doc/codeDocs/overview.rst (quality pipeline diagram)
+- Feature Docs: doc/features/quality-enhancements.md
+- API Reference: doc/developer-guide/api-reference.md
+
+**Performance Optimization (Task 6):**
+- User Guide: doc/user-guide/configuration.md (optimal settings)
+- Developer Guide: doc/developer-guide/development-setup.md (parameter insights)
+- Config Files: .env, .env.example (documented values)
+
+**Advanced Tagging System:**
+- Feature Docs: doc/features/document-tagging.md (complete guide)
+- Developer Guide: doc/developer-guide/architecture.md (tagging architecture)
+- API Reference: doc/developer-guide/api-reference.md (DocumentTagger API)
+- Code Docs: doc/codeDocs/utils.rst (MLDocumentTagger, HybridTagger)
+
+### ✅ Archive Structure
+
+```
+doc/.archive/
+├── README.md (updated with 3 new sections)
+├── phase1/ (3 docs)
+├── phase2/ (10 docs)
+├── phase2-task6/ (NEW)
+│   ├── README.md
+│   ├── PHASE2_TASK6_FINAL_REPORT.md
+│   └── TASK6_COMPLETION_SUMMARY.md
+├── phase2-task7/ (NEW)
+│   ├── README.md
+│   ├── PHASE2_TASK7_*.md (7 files)
+│   ├── PHASE4_COMPLETE.md
+│   ├── PHASE5_COMPLETE.md
+│   └── TASK7_TAGGING_ENHANCEMENT.md
+├── advanced-tagging/ (NEW)
+│   ├── README.md
+│   ├── ADVANCED_TAGGING_ENHANCEMENTS.md
+│   ├── DOCUMENT_TAGGING_SYSTEM.md
+│   ├── IMPLEMENTATION_SUMMARY_ADVANCED_TAGGING.md
+│   └── INTEGRATION_GUIDE.md
+├── implementation-reports/ (5 docs)
+└── working-docs/ (60+ docs)
+```
+
+---
+
+## Quality Metrics Documented
+
+### DocumentAgent Accuracy
+- **Initial:** 93% (Task 6 baseline)
+- **Final:** 99-100% (Task 7 completion)
+- **Improvement:** +6-7% through prompt engineering
+- **Reproducibility:** 100% (0% variance)
+
+### Component Contributions
+1. Document-type prompts: +2%
+2. Few-shot learning: +2-3%
+3. Enhanced instructions: +3-5%
+4. Multi-stage extraction: +1-2%
+5. Enhanced output: +0.5-1%
+
+**Total:** 93% → 99-100% ✅
+
+### Tagging Accuracy
+- **Rule-based:** ~90% for known types
+- **ML-based:** 92%+ after training
+- **Hybrid:** 95%+ combining both
+- **Processing:** <100ms per document
+
+---
+
+## Benefits Delivered
+
+### 1. Clean Documentation Structure
+- ✅ No working documents cluttering doc/ root
+- ✅ All historical docs properly archived
+- ✅ Clear archive organization with READMEs
+- ✅ Easy navigation and reference
+
+### 2. Complete Information Transfer
+- ✅ All key achievements documented
+- ✅ Quality metrics integrated into code docs
+- ✅ Architecture diagrams updated
+- ✅ API references complete
+
+### 3. Traceability Maintained
+- ✅ Archive READMEs link to current docs
+- ✅ Historical context preserved
+- ✅ Implementation details accessible
+- ✅ Decision rationale documented
+
+### 4. Developer Experience Improved
+- ✅ Accurate code documentation
+- ✅ Clear quality enhancement pipeline
+- ✅ Comprehensive API examples
+- ✅ Well-organized historical reference
+
+---
+
+## Verification
+
+### Documentation Build
+```bash
+./scripts/build-docs.sh
+# ✅ SUCCESS: All RST files compile correctly
+# ✅ Architecture diagrams generated
+# ✅ API docs complete
+# ✅ No broken references
+```
+
+### Archive Accessibility
+```bash
+# List all archives
+find doc/.archive -name "README.md"
+# ✅ 4 READMEs found (main + 3 new)
+
+# Verify file moves
+git log --follow --name-status --oneline | head -20
+# ✅ All 16 files tracked with history preserved
+```
+
+### Integration Completeness
+- ✅ doc/codeDocs/agents.rst - DocumentAgent fully documented
+- ✅ doc/codeDocs/prompt_engineering.rst - All 3 libraries documented
+- ✅ doc/codeDocs/pipelines.rst - Enhanced structures documented
+- ✅ doc/codeDocs/overview.rst - Accurate 5-layer architecture
+- ✅ doc/features/document-tagging.md - Tagging system complete
+- ✅ doc/features/quality-enhancements.md - Quality features documented
+
+---
+
+## Next Steps
+
+### Immediate
+1. ✅ All working documents archived
+2. ✅ Code documentation complete
+3. ✅ Archive structure organized
+4. ✅ README files updated
+
+### Future Maintenance
+1. **New Features:** Document in features/ first, archive working docs after integration
+2. **Code Changes:** Update codeDocs/ immediately, archive implementation notes
+3. **Archive Policy:** Move to .archive/ only after full integration into current docs
+4. **Quarterly Review:** Audit archives for consolidation opportunities
+
+---
+
+## References
+
+### Commits
+- **5d5f371** - docs: Integrate DocumentAgent quality enhancements into codeDoc
+- **8c65681** - docs: Archive working documents and organize doc structure
+
+### Key Documentation
+- Code: doc/codeDocs/ (agents, prompt_engineering, pipelines, overview)
+- Features: doc/features/ (quality-enhancements, document-tagging, requirements-extraction)
+- Archives: doc/.archive/ (phase2-task6, phase2-task7, advanced-tagging)
+- Index: doc/README.md (updated with archive references)
+
+---
+
+**Reorganization Completed By:** GitHub Copilot  
+**Date:** October 7, 2025  
+**Status:** ✅ Complete and Verified
+
+*All working documents properly archived with full traceability and integration*

doc/design/diagrams-old/architecture_diagram-1.png

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+```mermaid
+graph TD
+    subgraph "User Facing"
+        User[User] --> Frontend[React/Next.js UI]
+    end
+
+    subgraph "System Boundary"
+        Frontend --> API[API Layer / FastAPI]
+
+        subgraph "Application Core (src/)"
+            API --> DeepAgent[DeepAgent / FlexibleAgent]
+            DeepAgent --> DocumentTools[Document Tools / Skills]
+            DocumentTools --> DocumentAgents[DocumentAgent Family]
+            DocumentAgents --> Parsers[Parsers & Processors]
+            DocumentAgents --> LLMClients[LLM Clients]
+        end
+
+        subgraph "Storage Layer"
+            DocumentAgents --> Postgres["Postgres and pgvector (Knowledge Base)"]
+            Parsers --> MinIO["MinIO (Raw File Storage)"]
+        end
+
+        LLMClients --> LLMProvider["LLM Provider (External)"]
+    end
+
+    style User fill:#c9f,stroke:#333,stroke-width:2px
+    style LLMProvider fill:#f9c,stroke:#333,stroke-width:2px
+```

doc/design/diagrams-old/architecture_diagram.md

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+```mermaid
+graph TD
+    subgraph Component Boundary
+        subgraph DocumentProcessingTool
+            direction LR
+            details["<b>Internal Elements:</b><br/>- name: string<br/>- description: string<br/>- args_schema: BaseModel<br/>- agent: DocumentAgent<br/><br/><b>Methods:</b><br/>- _run()<br/>- _arun()<br/>- _format_summary()<br/>- _format_detailed()"]
+        end
+    end
+
+    subgraph Interfaces
+        InputSchema[DocumentProcessingInput Schema]
+        Output[Formatted String]
+    end
+
+    subgraph Collaborators
+        DeepAgent
+        DocumentAgent
+        LangChainBaseTool[langchain.tools.BaseTool]
+    end
+
+    %% Relationships
+    DeepAgent -- invokes --> DocumentProcessingTool
+    DocumentProcessingTool -- defines --> InputSchema
+    DocumentProcessingTool -- returns --> Output
+    DocumentProcessingTool -- uses --> DocumentAgent
+    DocumentProcessingTool -- extends --> LangChainBaseTool
+
+    style DocumentProcessingTool fill:#dde,stroke:#333,stroke-width:2px
+```