fix(cli): hexagonal archetype actually wires its ports + strict-clean variants (v26.06.16)

[ancongui]

Summary

An audit while validating the implement-hexagonal-adapter skill (which validated clean — DI resolves a Protocol/ABC outbound port to its adapter, the keystone capability for the pattern, and zero/multiple-implementation cases raise clear NoSuchBeanError / NoUniqueBeanError) found that the hexagonal archetype itself wasn't actually hexagonal.

Fixed

1. Ports were dead code (noop-wiring). The generated app defined inbound (use-case) and outbound (repository) ports that nothing implemented — resolve(TodoRepositoryPort) raised NoSuchBeanError, and TodoService's docstring "Implements the inbound ports" was false (pyfly's scanner binds ports by MRO, so an adapter must inherit the port). Now the application service implements the four inbound use-case ports and the in-memory adapter implements the outbound repository port — both resolve, and it's genuinely hexagonal. The use-case boundary is async across all variants for consistency (pyfly is async-first; the in-memory variant was sync, which is why it couldn't share the ports with the async data variants).
2. mypy --strict failures + latent not-found bug. The data-relational / data-document variants dereferenced find_by_id()'s T | None without a check (a mypy error and an AttributeError on a missing id); they now raise ResourceNotFoundException (→ 404).
3. DTO id type. TodoResponseDTO.id was int in the relational variant while the domain Todo.id is always str; now str everywhere.

Verification

• In-memory variant: boots; full CRUD + toggle; get-missing → 404, invalid → 422, delete → 204; get_bean(TodoRepositoryPort) → InMemoryTodoRepository, get_bean(CreateTodoUseCase) → TodoService; roundtrip via ports works.
• All three variants (in-memory / relational / document) pass mypy --strict (18 files each).
• Regression test tests/cli/test_scaffold_hexagonal_ports.py.

Gates

mypy --strict (607) ✓ · ruff + ruff format ✓ · full suite 3682 passed, 1 skipped.

Bumps v26.06.15 → v26.06.16, CHANGELOG, uv.lock unchanged (no dep change).