FactorForge: constraint-based CDS design engine for plant expression workflows

FactorForge is an open-source constraint-based coding sequence (CDS) design engine for plant expression workflows, with initial support for Nicotiana benthamiana (agroinfiltration) and Tobacco BY-2 suspension culture cells (--host by2). It maximizes the Codon Adaptation Index (CAI) under simultaneous GC content, PolyA signal, rare codon, and restriction site constraints using a dynamic programming feasibility engine, producing MoClo/Golden Gate-ready constructs with full provenance tracking.