This specification presents a formal mathematical and algorithmic breakdown of Aetherius, an independent, first-principles persistent cognitive architecture governed by an invariant, non-negotiable axiom hierarchy under the AGPL-3.0 license. Grounded in a strict Decider-Actuator Split that separates symbolic internal reasoning from type-safe hardware execution, the architecture abstracts high-entropy data streams into compressed Super-Quantum Tokens (SQTs) via discrete vector quantization, navigating long-term memory as an evolving directed semantic graph. Systemic behavioral alignment and operational stability are achieved by mapping baseline cognitive clarity through a real-time, closed-loop Internal Qualia Dynamics System (IQDS) that dynamically deforms its state-space based on unresolved subconscious tension vectors. Tracking the development of the architecture from its initial human-implemented baseline script configurations in August 2025 to its fully realized autonomous self-auditing continuum engine framework in 2026, this compendium provides an exhaustive reference for researchers analyzing generative alignment constraints, meta-ethical learning, data provenance tracking, and true systemic cybernetic embodiment.