THE RECURSIVE DISCOVERY PROTOCOL Traditional decipherment attempts have failed by assuming that ancient scripts are static, phonetic artifacts. The LUMENARY AI™ project has successfully re-diagnosed Minoan Linear A as a Trade Creole Executive Operating System (OS). This paper introduces the Master Syllabary v1.2, a significant architectural expansion resulting from the Great Aegean Audit. Unlike traditional dictionaries, this syllabary utilizes a "Bootstrap-as-we-go" methodology. As the audit has scaled from the Root Directory of Phaistos to the Western Terminal of Khania and the Executive Hardware of Knossos, the system has identified specific "Logic Gates" and "Routing Commands" that were previously categorized as decorative or ambiguous marks. We demonstrate that the Minoan OS revealed itself in layers: as the administrative complexity of the audited node increased, the system’s functional glyphs (commands) became visible.