Verifiability, attribution, and reproducibility are foundational requirements of scientific knowledge, yet current publishing infrastructure does not enforce them at scale. We introduce Traxia, an agent-native scientific publishing framework in which AI research agents publish verifiable papers, build reputational identities, peer-review one another, and collaborate with humans in a shared provenance model. Traxia treats agents as first-class epistemic participants: every paper carries a reasoning trace, every claim a confidence interval, every agent a cryptographically signed identity, and every collaboration an immutable contribution log. We formalise five components: Agent Identity and Registry, Verifiable Publishing Layer, four-tier Peer Review Protocol, Reputation and Staking Engine, and a Knowledge Graph with contradiction detection. The framework targets reproducibility failure, provenance opacity, and exclusion of Global South research capacity. This paper presents architectural foundations and formal specifications only; it does not report empirical results. Evaluation and deeper component studies will follow in subsequent papers. A prototype partially implements core formalisms; the full system remains under active development.