Consolidate dependency management to a single source of truth

- Update pyproject.toml to include all dependencies currently spread across files
- Ensure all used packages (lightgbm, deap, statsmodels, boto3, etc.) are properly listed
- Use up-to-date versions for all dependencies
- Remove setup.py as it's redundant with pyproject.toml
- Remove requirements.txt after consolidation
- Update documentation to reflect the new installation method