AI-generated software changes make it increasingly important to determine what a change preserves, where local consistency fails to extend globally, and which alternatives remain. We develop the foundations of Algebraic Architecture Theory (AAT) from Atoms, typed primitive facts, and Laws, equations that objects must satisfy. A reading specifies what counts as structure and which operations and laws to preserve. The main reconstruction theorem identifies the category of full geometries and all their structure-preserving morphisms with an independently defined category of local models, up to equivalence. Objects are recovered up to isomorphism and morphisms between fixed endpoints uniquely. The theory addresses gluing, diagnosis, transport, classification of changes, and reconstruction. From finite Atom families we construct cores closed under operations and geometries with sites and coefficients. We give conditions under which a Cech obstruction detects the existence of a global state and, through comparison with repair semantics, a global repair. We compare diagnoses and give a finite criterion for uniform invariance given computable finite data. Transport along exact changes has a universal property and commutes with base change on exact pointed pullback squares. Comparisons of routes generated from the same square, finite comparison diagram, and geometry factor into an invertible comparison and an idempotent normalization. We characterize when observations determine comparison preservation and classify compatible lifts. Encodings of lens and protocol semantics preserve and reflect laws and recover semantics-preserving morphisms. Applications classify and count operation-preserving changes and extend morphisms uniquely from finite tables. Corresponding Lean declarations are listed in the appendix.

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