Specification Gaps in Physical Theory: A Systems Engineering Audit of Undefined Primitives

Systems engineering audit treating physics as a deployed formal specification and evaluating it against standard completeness criteria from software engineering (IEEE 830), hardware certification (ISO 9001), and safety-critical systems (DO-178C). Identifies five categories of undefined primitives — entities the specification requires but cannot define within its own formalism: the observer needed for quantum measurement, initial and boundary conditions injected without derivation, semantic content and phenomenal experience categorically absent from physical variables, agency and goal-directedness missing from state descriptions, and counterfactual possibility spaces not represented as physical objects. Each gap maps to known foundational problems: measurement problem, fine-tuning, hard problem of consciousness, free will, and quantum contextuality respectively. The central finding is that these are not independent mysteries but predictable failure modes of a single structural condition — specification incompleteness. The paper explicitly distinguishes itself from Godel-for-physics arguments, intelligent design, and god-of-the-gaps reasoning. No claims are made about what fills the gaps. The audit documents architecture; interpretation is left to others. The framework is maximally neutral: it applies engineering methodology to foundational physics without taking positions on metaphysics, theology, or resolution strategies. Physics is shown to be extraordinarily successful within its declared scope but incomplete relative to its implicit claim of universal fundamental description.