XScientist: A Git-Like Research Protocol for Long-Running Autonomous Scientific Discovery

Autonomous research systems can generate plausible papers while losing the decisions, failed branches, and evidence needed to inspect or continue the work. We present XScientist, a local-first, git-like protocol that treats research state, rather than a manuscript, as the unit of continuation. Hypotheses, experiment attempts, observations, claims, reviews, and handoffs are represented as typed, content-addressed objects in an exploration graph. Immutable checkpoints, explicit negative outcomes, claim-evidence closure, replay boundaries, and authority-aware gates make each transition inspectable without treating a passing integrity check as scientific truth. The protocol exports a portable Agent-Native Research Artifact (ARA) that another agent or human can inspect, fork, verify, and extend. A reference implementation integrates planning, execution, review, repair, and supervised long-running operation while preserving provenance across these stages. We evaluate the protocol with controlled artifact-integrity workloads and matched external task pilots, keeping native task performance separate from evidence and audit claims. The result is an interoperability and accountability layer for long-running autonomous science, with explicit boundaries where human judgment and independent evaluation remain necessary.