Add FA diagnostic protocol reference implementation

Codex round 15 #1 priority for the E&D-track paper:
  - protocol/protocol.py: 4 diagnostics (residual norms, BP grad norms,
    cross-batch direction stability, and a frozen-baseline comparator)
  - protocol/report.py: DiagnosticReport with per-diagnostic verdicts and
    pretty-printer
  - protocol/smoke_test.py: validates BP/DFA/EP checkpoints produce the
    expected verdicts (BP/EP trustworthy; DFA walked back via residual
    explosion + BP grad at floor)
  - protocol/README.md: usage, audit cases, threshold rationale
  - protocol/CHECKLIST.md: 6 evaluation pipeline pitfalls (norm(-1),
    cosine_similarity eps clamp, fp16 underflow, Bs reproducibility,
    aggregation, layer-0 dominance)
  - protocol/REPORTING_TEMPLATE.md: per-method fillable form for FA papers

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