bitscopic/BIAS-2015: v3.1.0

This release introduces a new allele-frequency cutoff cascade for BA1/BS1/PM2: gene-specific VCEP overrides (ClinGen CSpec) → derived missense O/E upper × MOI cutoffs → flat fallback values, and wires it through the BIAS classifiers/dataset loading. It also adds calibration/plotting scripts and smoke tests to exercise the new lookup and parsing logic. Changes: Add VCEP AF cutoff generation + runtime lookup (including popmax computation) and integrate VCEP overrides into BA1/BS1/PM2 classifiers. Fixed edge cases of PVS1, added more robust checks for NMD. Add missense O/E upper × MOI cutoff resolution utilities and pass the required datasets through the classification pipeline. Add calibration pipeline scripts + plots and a smoke-test module for the new behavior.