Semantic Tax: Coordination Overhead in Prokaryotic Genomes — Reproducibility Code and Data

Version 3.1.0 corrected reproducibility release for the manuscript "Coordination Overhead as a Macro-Genomic Phenotype in Prokaryotes." This release replaces the v3.0.0 executable-script bug with a clean, self-contained archive and uses a homogeneous eggNOG-mapper 2.1.13+galaxy0 annotation set (eggNOG database 5.0.2, Galaxy Europe) as the primary Table 2 source, covering all 330 selected genomes. Four recovered eggNOG-mapper v2.1.8 outputs (200 genomes) are retained as drift comparators only; the four-batch overlap audit shows operationally negligible mapper-version drift (largest kappa slope difference 0.0004; per-genome max |delta-kappa| 0.00123). The single displayed Table 2 change from v3.0.0 is the kappa OLS slope: 0.96 -> 0.97, a precision/rounding correction surfaced by rebuilding the reproducible archive. All other reported metrics round identically at two decimal places. Bundle contents: 7 primary v2.1.13 annotation files, 4 v2.1.8 drift comparators, 17-field provenance manifest with SHA-256 checksums and role labels, paired kappa CSV, replication result tables, V x X regression outputs, per-genome X-extended dataframe, drift summary, README, version notes, and SHA256SUMS. Dataset: 2,295 genomes for the V x X analysis; 330 genomes for the eggNOG replication. COG-X is treated as an internal mobilome/prophage/transposon annotation proxy, not independent ecological validation. Supersedes v3.0.0 (10.5281/zenodo.19962294).Minor post-publication file correction: release-process residue and stale documentation were removed; environment and licensing documentation were added; and the Table 2 recomputation script's p-value calculation was corrected to reproduce the finite canonical values. Underlying annotation files, paired data, canonical regression outputs, and all manuscript-reported estimates are unchanged.