Code cleanup and file organization

Fixes:
- Fixed mypy.ini boolean values (lowercase true/false)
- Fixed unreachable code in data_integrity.py encode/decode methods
- Updated import ignores for smbus and skimage

Examples reorganization:
- Renamed advanced_integration_example.py -> integration_example.py
- Renamed multi_protocol_example.py -> protocol_demo.py

Docs consolidation:
- Removed duplicate api_reference.md (kept api_documentation.md)
- Removed duplicate protocols_index.md (kept protocols.md)

All 322 tests pass

Author: muditbhargava66