CIAT/Cleaned_batch-2: CLEANED Development Changes (2025)

This release consolidates all development updates made to the CLEANED package during 2025. The update improves model robustness, internal consistency, and alignment between variable inputs, calculations, and reported outputs. Key updates include corrections to nitrogen fixation logic, improved selection of methane emission factors, standardized variable naming to match JSON outputs, removal of redundant variables, and enhancements to protein requirement and meat production calculations. Annual livestock outputs were expanded to include animal manure production. All changes are fully documented in the commit history.