🚀 SIMPLICITY v2.2.4: Heterogeneous Populations This major release marks the integration of the long-shedders branch, evolving SIMPLICITY from an acute-infection model into a framework capable of handling population heterogeneity. ✨ Highlights & New Features Heterogeneous Population Modeling: Added full support for mixed populations containing both "Standard" and "Long-Shedder" host types. The model now features distinct infectiousness windows, detectability profiles, and lineage capacities for each sub-population. Evolutionary Calibration: This accounts for the compound evolutionary pressure generated by the continuous emergence of intra-host lineages ($k_v$) over time in distinct host types. Automated Calibration Pipeline 🧹 Housekeeping & Archiving (Important!) To keep the root and scripts/ directories clean for version 2.0+, we performed a massive repository cleanup: Paper Archive: All specific figure-generating scripts and legacy experiments used for the original SIMPLICITY publication have been safely moved to scripts/00_SIMPLICITY_paper_archive/. Test Suite: Removed obsolete tests and added new, robust test files (e.g., tests/test_diag_mut_rates.py) to validate the new parameterization logic.