This document presents the first manifesto for “version-controlled science,” a perspective in which scientific theories are treated not as static artifacts but as evolving structures with explicit histories. It introduces key concepts such as epistemic commits, semantic diffs, theoretical branches, and lineage-aware repositories. The manifesto argues that modern scientific practice distributed, iterative, and computationally intensive requires representational forms that make conceptual evolution visible and traceable. It outlines the limitations of static publication models and proposes a shift toward versioned, lineage-aware scientific records. This v1.0 release includes a structured framework, a comparative analysis between static and version-controlled approaches, a real case study (MDPA v1→v2), and a call to action toward a more transparent and evolution-aware scientific ecosystem.