TM-Spec (Third Matter Specification) is a YAML/JSONL metalanguage and reference toolchain for describing structures, defects, magnetic state, environment, reaction networks, DFT/MLIP calculations, workflows, sanity gates, and provenance of atomistic simulations in a single human-readable, schema-validated document. It is designed for paper Supporting Information, ephemeral cloud compute, and cross-code reproducibility (Quantum ESPRESSO, CP2K, ABACUS, GPAW, MACE, CHGNet).