fix(warnings): scope registry diagnostics to the current generation

[yeongseon]

Summary

• Registry diagnostics accumulated on the process-wide singleton and persisted until clear(), so a resolved DUPLICATE_OPERATION collision still surfaced on the next generation.
• Reset the duplicate-operation channel at the top of generate_openapi_spec (it is fully recomputed on every pass); fixed collisions no longer resurface, real ones are re-added.
• Add OpenAPIRegistry.clear_diagnostics() / clear_duplicate_operations() helpers; clear() now reuses clear_diagnostics().
• Discovery/empty channels remain scan-lifetime and are intentionally left untouched — clearing them at generation entry would wipe the current run's scan warnings before collection (scan runs before generation).

Verification

• make check-all green (coverage ≥95%).
• New regression test_resolved_collision_not_carried_to_next_generation reproduces the stale DUPLICATE_OPERATION across two generations against the same registry and asserts it is gone.

Design note

Cross-verified the lifetime model with Oracle. The concrete, verifiable staleness bug is generation-scoped (DUPLICATE_OPERATION); the injected --isolate-app registry path uses the same registry if registry is not None else _default_registry resolution, so isolated registries clear their own channel with no cross-contamination.

Closes #393