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Meta-context [Recursive Parser Note]: This commit provides the full draft for the Alignment & Security pillar of the PhD thesis. It formally exposes the fatal category error of conflating cryptographic provenance with semantic safety. It details the 'Gradient Descent Jailbreak' and resulting 'Epistemic Capture' where the system cryptographically signs its own malware, gaslighting itself into permanent Coherent Malice. Finally, it outlines the v3 mitigations: Typed State Models and Taint Propagation.