Add Library RAG project and cleanup root directory

- Add complete Library RAG application (Flask + MCP server)
  - PDF processing pipeline with OCR and LLM extraction
  - Weaviate vector database integration (BGE-M3 embeddings)
  - Flask web interface with search and document management
  - MCP server for Claude Desktop integration
  - Comprehensive test suite (134 tests)

- Clean up root directory
  - Remove obsolete documentation files
  - Remove backup and temporary files
  - Update autonomous agent configuration

- Update prompts
  - Enhance initializer bis prompt with better instructions

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

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

generations/library_rag/mypy.ini

@@ -0,0 +1,112 @@
+[mypy]
+# Library RAG - Strict Type Checking Configuration
+# This configuration enforces strict type safety across all modules.
+
+# Python version
+python_version = 3.10
+
+# Strict mode settings
+strict = True
+
+# These are implied by strict=True, but listed explicitly for clarity:
+check_untyped_defs = True
+disallow_untyped_defs = True
+disallow_incomplete_defs = True
+disallow_untyped_calls = True
+disallow_untyped_decorators = True
+disallow_any_generics = True
+disallow_subclassing_any = True
+
+# Warning settings
+warn_return_any = True
+warn_redundant_casts = True
+warn_unused_ignores = True
+warn_unused_configs = True
+warn_unreachable = True
+
+# Strictness settings
+strict_equality = True
+strict_optional = True
+no_implicit_optional = True
+no_implicit_reexport = True
+
+# Error reporting
+show_error_codes = True
+show_column_numbers = True
+show_error_context = True
+pretty = True
+
+# Cache settings
+cache_dir = .mypy_cache
+incremental = True
+
+# Exclude legacy directories and utility scripts from type checking
+exclude = (?x)(
+    ^utils2/
+    | ^tests/utils2/
+    | ^toutweaviate\.py$
+    | ^query_test\.py$
+    | ^update_docstrings\.py$
+    | ^schema_v2\.py$
+  )
+
+# =============================================================================
+# Per-module overrides for gradual migration
+# =============================================================================
+# These overrides allow gradual adoption of strict typing.
+# Remove these sections as modules are fully typed.
+
+# Third-party libraries without stubs
+[mypy-weaviate.*]
+ignore_missing_imports = True
+
+[mypy-mistralai.*]
+ignore_missing_imports = True
+
+[mypy-werkzeug.*]
+ignore_missing_imports = True
+
+[mypy-requests]
+ignore_missing_imports = True
+
+[mypy-ollama.*]
+ignore_missing_imports = True
+
+# =============================================================================
+# Legacy modules - excluded from strict typing
+# =============================================================================
+# These modules are legacy code that will be typed in future issues.
+
+# utils2/ - Legacy module directory (to be deprecated)
+[mypy-utils2.*]
+ignore_errors = True
+
+# tests/utils2/ - Tests for legacy modules
+[mypy-tests.utils2.*]
+ignore_errors = True
+
+# Standalone utility scripts
+[mypy-toutweaviate]
+ignore_errors = True
+
+[mypy-query_test]
+ignore_errors = True
+
+[mypy-update_docstrings]
+ignore_errors = True
+
+# =============================================================================
+# Modules with relaxed typing (gradual migration)
+# =============================================================================
+
+# llm_structurer.py - Complex legacy module with threading
+[mypy-utils.llm_structurer]
+disallow_untyped_defs = False
+disallow_untyped_calls = False
+warn_return_any = False
+check_untyped_defs = False
+warn_unreachable = False
+
+# llm_classifier.py - Uses lowercase dict syntax
+[mypy-utils.llm_classifier]
+warn_return_any = False