"""
Integrated feature/trait matrix v2 (produces feature_matrix_v2.csv, 2,919 x 79).
Merges the original feature matrix with all revision outputs: four independent binary traits
(trait_halophily/methanogenesis/thermophily/acidophily), MCR metabolism classification
(canonical methanogenesis vs alkane ACR/ANME), full Wood-Ljungdahl module status, and completeness flags.
Inputs: feature_matrix.csv, trait_matrix.csv, mcr_classification.csv, wood_ljungdahl_modules.csv,
pathway_completeness.csv, genome_panel.csv, dereplication.csv, proteome_composition.csv, env_metadata.csv,
marker_matrix.csv, and marker .domtbl files.
"""