docs: Update README with complete script documentation

- Add all available uv run scripts from pyproject.toml to Quick Start section
- Include build, build-all, build-sparse, setup-datasets commands
- Add upload scripts for deployment (upload-framework, upload-indexes, upload-vdrs)
- Document testing commands (run-e2e-tests, test-legal-coreference)
- Update project structure to reflect actual scripts directory contents
- Enhance troubleshooting section with new build and test commands

Resolves documentation gap between available scripts and README content

README.md

@@ -360,10 +360,26 @@ uv run streamlit run app/main.py  # Run the app
 # Option 3: Development mode with auto-reload
 uv run streamlit run app/main.py --server.runOnSave true
 
-# Option 4: Additional build commands for advanced features
+# Option 4: Build commands for advanced features
+uv run download-models            # Pre-download transformer models locally
 uv run build-indexes              # Build search indexes (FAISS, BM25)
 uv run build-graphs               # Build knowledge graphs with entity resolution
-uv run download-models            # Pre-download transformer models locally
+uv run build-sparse               # Build BM25 sparse indexes
+uv run build                      # General build script
+uv run build-all                  # Comprehensive build pipeline (all indexes + graphs)
+
+# Option 5: Data management commands
+uv run setup-datasets             # Setup initial datasets
+
+# Option 6: Upload commands (for deployment)
+uv run upload-framework           # Upload DD framework
+uv run upload-indexes             # Upload search indexes
+uv run upload-vdrs                # Upload VDR data
+
+# Option 7: Testing commands
+uv run verify-test-coverage       # Verify critical test coverage
+uv run run-e2e-tests              # Run end-to-end tests
+uv run test-legal-coreference     # Test legal coreference resolution
 ```
 
 ### Environment Setup (for AI features)
@@ -755,10 +771,16 @@ dd_poc/
 │   ├── build_sparse_indexes.py # BM25 sparse index construction
 │   ├── build.py              # General build script
 │   ├── download_models.py    # Download and cache transformer models
+│   ├── run_e2e_tests.py      # End-to-end test runner
+│   ├── setup_datasets.py     # Initial dataset setup
 │   ├── start.py              # 🚀 Launch script (Python)
+│   ├── streamlit_cloud_config.py # Streamlit Cloud configuration
 │   ├── test_entity_resolution.py # Entity resolution testing and validation
 │   ├── test_legal_coreference.py # Legal coreference testing
 │   ├── transformer_extractors.py # Transformer-based extraction utilities
+│   ├── upload_dd_framework.py # Upload DD framework for deployment
+│   ├── upload_dd_indexes.py  # Upload search indexes for deployment
+│   ├── upload_dd_vdrs.py     # Upload VDR data for deployment
 │   └── verify_test_coverage.py # Test coverage verification
 ├── tests/                    # 🧪 Comprehensive test suite
 │   ├── unit/                # Unit tests with entity processing tests
@@ -979,6 +1001,12 @@ uv run build-indexes && echo "✅ Search indexes built successfully"
 # Build knowledge graphs with entity resolution
 uv run build-graphs && echo "✅ Knowledge graphs built with entity resolution"
 
+# Build all indexes and graphs comprehensively
+uv run build-all && echo "✅ All indexes and graphs built successfully"
+
+# Run comprehensive test suite
+uv run run-e2e-tests && echo "✅ E2E tests completed"
+
 # Verify test coverage for critical workflows
 uv run verify-test-coverage