SOF Diagnostic Protocol

Paper XII of the RIME program introduces the SOF Diagnostic Protocol, a deployable methodology for producing structured diagnostic reports from sectorized observable analyses.Its standard output is a versioned SOF Diagnostic Report governed by the SOF Report Specification (SOFRS) v1.0. Each report records eight diagnostic fields: Sectorization, Observable Family, Support Matrix, Bridge Matrix, Repair Matrix, Wall Record, Claim Status, and Failure Modes. A trajectory summary is recorded inside the Wall Record when a deformation path is supplied.The protocol supports both white-box or realizational diagnostics and behavioral API-level diagnostics. Case studies include transformer activations, pretrained Qwen attention heads, mixture-of-experts routing, diffusion denoising, dynamic maze topology, recommender coverage dead zones, and an API-only language model. Boundary cases demonstrate when a report is inapplicable, degenerate, uninformative, or dominated by infrastructure failure.A SOF Report is relative to its declared sectorization, observable family, and reporting specification. SOFRS standardizes the diagnostic artifact, but protocol conformance does not by itself establish the scientific adequacy of a domain realization. Domain-specific sectorizations and observables still require subject-matter justification.Paper XII does not propose a new theory of neural networks, quantum systems, control, or stochastic processes. It proposes a common, versioned diagnostic reporting protocol for systems admitting compatible sectorizations or stable diagnostic probe partitions. Source repository: https://github.com/dooven-prime/rime-lite This work is part of the Representation-Induced Mechanics and Evolution (RIME) research program.