docs: formalize phase 1 architecture

[TrueAlpha-spiral]

Formalized the documentation for TrueAlphaSpiral Phase 1 by confirming the existence of the Architectural Manifest and Prime Invariant documents, mapping the foundational concepts (Process Science, Computational Masonry) to the structural anatomy.

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PR created automatically by Jules for task 11569791183772185890 started by @TrueAlpha-spiral

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